Starting phenix.real_space_refine
on Tue Jul 29 17:35:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwe_20506/07_2025/6pwe_20506.cif"
  }
  resolution = 3.95
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      14      5.16       5
     C    6576      2.51       5
     N    2231      2.21       5
     O    2808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11923
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 626
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 789
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 743
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Restraints were copied for chains:
    E, F, G, H
  Time building chain proxies: 8.50, per 1000 atoms: 0.71
  Number of scatterers: 11923
  At special positions: 0
  Unit cell: (108.36, 113.4, 120.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     294     15.00
     O    2808      8.00
     N    2231      7.00
     C    6576      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: 2.96
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      59.4% alpha, 1.6% beta
      95 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 5.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
    Processing helix  chain 'A' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 105
      removed outlier: 3.841A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 3.602A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 128
      removed outlier: 3.589A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 39
      removed outlier: 3.533A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.853A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.699A  pdb=" N   ALA C  20 " --> pdb=" O   ARG C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU C  32 " --> pdb=" O   ARG C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 3.700A  pdb=" N   ALA C  51 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU C  63 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN C  67 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA C  68 " --> pdb=" O   LEU C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU C  82 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN C  83 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS C  94 " --> pdb=" O   GLU C  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 43
      removed outlier: 3.690A  pdb=" N   ILE D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS D  40 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS D  43 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN D  60 " --> pdb=" O   MET D  56 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ALA D  72 " --> pdb=" O   GLU D  68 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR D  80 " --> pdb=" O   ARG D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LYS D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 50
    Processing helix  chain 'E' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU E  70 " --> pdb=" O   PRO E  66 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 105
      removed outlier: 3.842A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN E  93 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU E  94 " --> pdb=" O   MET E  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 113
      removed outlier: 3.601A  pdb=" N   HIS E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 128
      removed outlier: 3.590A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 39
      removed outlier: 3.534A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.854A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.698A  pdb=" N   ALA G  20 " --> pdb=" O   ARG G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU G  32 " --> pdb=" O   ARG G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 3.701A  pdb=" N   ALA G  51 " --> pdb=" O   PRO G  47 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL G  53 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU G  63 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY G  66 " --> pdb=" O   LEU G  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN G  67 " --> pdb=" O   GLU G  63 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA G  68 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU G  82 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLN G  83 " --> pdb=" O   PRO G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS G  94 " --> pdb=" O   GLU G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 43
      removed outlier: 3.689A  pdb=" N   ILE H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS H  40 " --> pdb=" O   ILE H  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS H  43 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN H  60 " --> pdb=" O   MET H  56 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ALA H  72 " --> pdb=" O   GLU H  68 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG H  76 " --> pdb=" O   ALA H  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR H  80 " --> pdb=" O   ARG H  76 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER H 109 " --> pdb=" O   LYS H 105 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LYS H 113 " --> pdb=" O   SER H 109 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.787A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42
      removed outlier: 7.109A  pdb=" N   ARG C  41 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.536A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42
      removed outlier: 7.395A  pdb=" N   ARG G  41 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77

    206 hydrogen bonds defined for protein.
    600 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      225 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      95 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 3.71

  Time building geometry restraints manager: 3.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 1843
        1.32 -     1.44: 4466
        1.44 -     1.56: 5815
        1.56 -     1.68: 586
        1.68 -     1.80: 26
  Bond restraints: 12736
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.482 -0.060 3.00e-02 1.11e+03 3.98e+00
  bond pdb=" CB  PRO A  66 "
       pdb=" CG  PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.09e+00
  bond pdb=" CB  PRO E  66 "
       pdb=" CG  PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.06e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C3'  DG I  38 "
       pdb=" O3'  DG I  38 "
    ideal  model  delta    sigma   weight residual
    1.422  1.373  0.049 3.00e-02 1.11e+03 2.68e+00
  ... (remaining 12731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 17147
        1.74 -     3.49: 1166
        3.49 -     5.23: 120
        5.23 -     6.97: 16
        6.97 -     8.71: 12
  Bond angle restraints: 18461
  Sorted by residual:
  angle pdb=" C   ARG H  30 "
        pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C   ARG D  30 "
        pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.24   -8.70 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
        pdb=" CB  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.07   -6.58 1.69e+00 3.50e-01 1.52e+01
  angle pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
        pdb=" CB  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.03   -6.54 1.69e+00 3.50e-01 1.50e+01
  angle pdb=" C   ALA C 102 "
        pdb=" N   GLN C 103 "
        pdb=" CA  GLN C 103 "
      ideal   model   delta    sigma   weight residual
     122.46  127.42   -4.96 1.41e+00 5.03e-01 1.24e+01
  ... (remaining 18456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.76: 5440
       31.76 -    63.52: 1415
       63.52 -    95.29: 44
       95.29 -   127.05: 0
      127.05 -   158.81: 3
  Dihedral angle restraints: 6902
    sinusoidal: 4744
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  LYS D  29 "
           pdb=" C   LYS D  29 "
           pdb=" N   ARG D  30 "
           pdb=" CA  ARG D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.05  -52.95     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  LYS H  29 "
           pdb=" C   LYS H  29 "
           pdb=" N   ARG H  30 "
           pdb=" CA  ARG H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.10  -52.90     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  ARG D  30 "
           pdb=" C   ARG D  30 "
           pdb=" N   LYS D  31 "
           pdb=" CA  LYS D  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.19   39.81     0      5.00e+00 4.00e-02 6.34e+01
  ... (remaining 6899 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1265
       0.044 -    0.088: 667
       0.088 -    0.133: 129
       0.133 -    0.177: 27
       0.177 -    0.221: 10
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CB  VAL G 106 "
            pdb=" CA  VAL G 106 "
            pdb=" CG1 VAL G 106 "
            pdb=" CG2 VAL G 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  VAL C 106 "
            pdb=" CA  VAL C 106 "
            pdb=" CG1 VAL C 106 "
            pdb=" CG2 VAL C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  VAL C  99 "
            pdb=" CA  VAL C  99 "
            pdb=" CG1 VAL C  99 "
            pdb=" CG2 VAL C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 1318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "   -0.046 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A  66 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  65 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO E  66 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E  66 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E  66 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H 101 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   GLY H 101 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLY H 101 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU H 102 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1315 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2734
        2.79 -     3.32: 10074
        3.32 -     3.85: 22518
        3.85 -     4.37: 26262
        4.37 -     4.90: 37230
  Nonbonded interactions: 98818
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OH  TYR H  37 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   TYR F  51 "
            pdb=" NH1 ARG F  55 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   TYR B  51 "
            pdb=" NH1 ARG B  55 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N2   DG I  21 "
            pdb=" O2   DC J -21 "
     model   vdw
     2.330 2.496
  ... (remaining 98813 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             2.240
  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:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     34.760
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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      :  0.010   0.088  12736  Z= 0.416
  Angle     :  0.929   8.715  18461  Z= 0.526
  Chirality :  0.053   0.221   2098
  Planarity :  0.007   0.069   1318
  Dihedral  : 27.121 158.809   5510
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.42 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

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: -6.65 (0.18), residues: 728
  helix: -4.66 (0.11), residues: 440
  sheet:  None (None), residues: 0
  loop : -3.73 (0.27), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS H 106 
 PHE   0.019   0.003   PHE A 104 
 TYR   0.018   0.004   TYR F  51 
 ARG   0.008   0.001   ARG H  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31222 (  431)
  hydrogen bonds       : angle      11.97429 ( 1038)
  covalent geometry    : bond        0.00952 (12736)
  covalent geometry    : angle       0.92883 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7194 (tt0) cc_final: 0.6709 (tp30)
REVERT: B   31 LYS cc_start: 0.8599 (tttt) cc_final: 0.8096 (mptt)
REVERT: B   51 TYR cc_start: 0.8455 (m-80) cc_final: 0.7977 (m-80)
REVERT: B   79 LYS cc_start: 0.7955 (mttp) cc_final: 0.7747 (mtpt)
REVERT: C  109 ASN cc_start: 0.7057 (t0) cc_final: 0.6806 (m-40)
REVERT: D   48 ASP cc_start: 0.8152 (p0) cc_final: 0.7794 (p0)
REVERT: D  106 HIS cc_start: 0.7772 (m90) cc_final: 0.7565 (m-70)
REVERT: E   41 TYR cc_start: 0.8455 (m-80) cc_final: 0.8156 (m-80)
REVERT: E   49 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7270 (tpp-160)
REVERT: E  118 THR cc_start: 0.9373 (m) cc_final: 0.9075 (p)
REVERT: F   80 THR cc_start: 0.8638 (m) cc_final: 0.8278 (p)
REVERT: F   84 MET cc_start: 0.6704 (mmm) cc_final: 0.6013 (mmm)
REVERT: F   88 TYR cc_start: 0.8433 (m-10) cc_final: 0.7793 (m-80)
REVERT: F   98 TYR cc_start: 0.8948 (m-10) cc_final: 0.8633 (m-10)
REVERT: H   40 LYS cc_start: 0.9155 (mttt) cc_final: 0.8815 (mtpt)
REVERT: H   80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7496 (m-10)
REVERT: H   97 LEU cc_start: 0.8873 (mt) cc_final: 0.8648 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.3725
  time to fit residues: 121.6347
Evaluate side-chains
  171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0000
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
C  23 GLN
D  60 ASN
D  64 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  23 GLN
G  88 ASN
H  60 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.133692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110745 restraints weight = 23421.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.112588 restraints weight = 13759.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.113787 restraints weight = 9824.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12736  Z= 0.169
  Angle     :  0.626   5.640  18461  Z= 0.375
  Chirality :  0.037   0.181   2098
  Planarity :  0.005   0.046   1318
  Dihedral  : 30.744 158.655   4040
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.53 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.75 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

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: -4.96 (0.23), residues: 728
  helix: -3.11 (0.18), residues: 468
  sheet:  None (None), residues: 0
  loop : -3.34 (0.29), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 106 
 PHE   0.010   0.001   PHE E 104 
 TYR   0.015   0.001   TYR C  56 
 ARG   0.009   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06552 (  431)
  hydrogen bonds       : angle       3.40047 ( 1038)
  covalent geometry    : bond        0.00362 (12736)
  covalent geometry    : angle       0.62647 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 212
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.9060 (m-80) cc_final: 0.8817 (m-80)
REVERT: A   73 GLU cc_start: 0.7181 (tt0) cc_final: 0.6911 (tp30)
REVERT: B   31 LYS cc_start: 0.8853 (tttt) cc_final: 0.8348 (mptt)
REVERT: B   35 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7738 (tpp80)
REVERT: B   59 LYS cc_start: 0.8362 (tttt) cc_final: 0.8066 (tttt)
REVERT: B   82 THR cc_start: 0.8526 (t) cc_final: 0.8052 (m)
REVERT: B   88 TYR cc_start: 0.8250 (m-80) cc_final: 0.7522 (m-10)
REVERT: C  109 ASN cc_start: 0.7152 (t0) cc_final: 0.6800 (m-40)
REVERT: D   48 ASP cc_start: 0.7976 (p0) cc_final: 0.7566 (p0)
REVERT: F   84 MET cc_start: 0.6344 (mmm) cc_final: 0.4721 (tpp)
REVERT: F   88 TYR cc_start: 0.8265 (m-10) cc_final: 0.7636 (m-80)
REVERT: H   39 TYR cc_start: 0.7849 (t80) cc_final: 0.7568 (t80)
REVERT: H   40 LYS cc_start: 0.9053 (mttt) cc_final: 0.8365 (mtpt)
REVERT: H   65 ASP cc_start: 0.8537 (t70) cc_final: 0.8234 (t0)
REVERT: H   80 TYR cc_start: 0.8029 (m-10) cc_final: 0.7559 (m-10)
  outliers start: 12
  outliers final: 4
  residues processed: 217
  average time/residue: 0.2940
  time to fit residues: 84.5650
Evaluate side-chains
  164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 160
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain E residue   96 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.106501 restraints weight = 24347.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.108289 restraints weight = 14590.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.109460 restraints weight = 10519.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12736  Z= 0.214
  Angle     :  0.630   6.390  18461  Z= 0.369
  Chirality :  0.037   0.172   2098
  Planarity :  0.005   0.042   1318
  Dihedral  : 30.667 161.379   4040
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.28 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -4.15 (0.26), residues: 728
  helix: -2.45 (0.20), residues: 472
  sheet:  None (None), residues: 0
  loop : -3.08 (0.32), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 106 
 PHE   0.010   0.001   PHE E 104 
 TYR   0.015   0.002   TYR D  37 
 ARG   0.005   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06255 (  431)
  hydrogen bonds       : angle       3.21869 ( 1038)
  covalent geometry    : bond        0.00479 (12736)
  covalent geometry    : angle       0.63016 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8532 (mtp-110) cc_final: 0.7954 (mtp85)
REVERT: A   73 GLU cc_start: 0.7423 (tt0) cc_final: 0.6981 (tp30)
REVERT: B   31 LYS cc_start: 0.8767 (tttt) cc_final: 0.8340 (mptt)
REVERT: B   59 LYS cc_start: 0.8464 (tttt) cc_final: 0.8255 (tttt)
REVERT: B   82 THR cc_start: 0.8583 (t) cc_final: 0.8195 (m)
REVERT: B   84 MET cc_start: 0.8475 (tpp) cc_final: 0.8262 (tpp)
REVERT: B   88 TYR cc_start: 0.8151 (m-10) cc_final: 0.7491 (m-10)
REVERT: D   48 ASP cc_start: 0.8134 (p0) cc_final: 0.7806 (p0)
REVERT: F   84 MET cc_start: 0.6462 (mmm) cc_final: 0.5310 (tpp)
REVERT: F   88 TYR cc_start: 0.8349 (m-10) cc_final: 0.7674 (m-80)
REVERT: H   39 TYR cc_start: 0.7986 (t80) cc_final: 0.7563 (t80)
REVERT: H   54 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8487 (tptm)
REVERT: H   80 TYR cc_start: 0.8130 (m-10) cc_final: 0.7712 (m-10)
REVERT: H   98 LEU cc_start: 0.8534 (mp) cc_final: 0.8125 (mp)
  outliers start: 22
  outliers final: 13
  residues processed: 184
  average time/residue: 0.3077
  time to fit residues: 75.4904
Evaluate side-chains
  174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   57 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 33 optimal weight:    0.4980
   chunk 38 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0570
   chunk 28 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
C  93 ASN
E  93 GLN
G  72 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.135398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112215 restraints weight = 23778.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.113977 restraints weight = 14123.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.115203 restraints weight = 10216.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12736  Z= 0.147
  Angle     :  0.558   7.420  18461  Z= 0.331
  Chirality :  0.033   0.148   2098
  Planarity :  0.004   0.049   1318
  Dihedral  : 30.165 159.356   4040
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.16 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.06 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.16 (0.29), residues: 728
  helix: -1.81 (0.22), residues: 474
  sheet:  None (None), residues: 0
  loop : -2.39 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  46 
 PHE   0.007   0.001   PHE H  67 
 TYR   0.018   0.001   TYR D 118 
 ARG   0.006   0.001   ARG H  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05414 (  431)
  hydrogen bonds       : angle       2.64599 ( 1038)
  covalent geometry    : bond        0.00320 (12736)
  covalent geometry    : angle       0.55818 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7379 (tt0) cc_final: 0.6773 (tp30)
REVERT: B   31 LYS cc_start: 0.8539 (tttt) cc_final: 0.8205 (mptt)
REVERT: B   72 TYR cc_start: 0.8556 (m-80) cc_final: 0.8328 (m-80)
REVERT: B   82 THR cc_start: 0.8472 (t) cc_final: 0.8108 (m)
REVERT: B   88 TYR cc_start: 0.7948 (m-10) cc_final: 0.7437 (m-10)
REVERT: D   48 ASP cc_start: 0.7951 (p0) cc_final: 0.7602 (p0)
REVERT: F   84 MET cc_start: 0.6389 (mmm) cc_final: 0.5249 (tpp)
REVERT: F   88 TYR cc_start: 0.8287 (m-10) cc_final: 0.7683 (m-80)
REVERT: F   98 TYR cc_start: 0.9198 (m-10) cc_final: 0.8920 (m-80)
REVERT: H   56 MET cc_start: 0.7671 (mmm) cc_final: 0.6771 (mtt)
REVERT: H   80 TYR cc_start: 0.8064 (m-10) cc_final: 0.7665 (m-10)
  outliers start: 17
  outliers final: 11
  residues processed: 176
  average time/residue: 0.3076
  time to fit residues: 71.7524
Evaluate side-chains
  158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 92 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 78 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  93 GLN
C  93 ASN
G  23 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.106077 restraints weight = 24453.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.107800 restraints weight = 15045.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108925 restraints weight = 11050.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  12736  Z= 0.232
  Angle     :  0.638   8.527  18461  Z= 0.367
  Chirality :  0.037   0.160   2098
  Planarity :  0.005   0.049   1318
  Dihedral  : 30.557 161.297   4040
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.22 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 18.77 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -3.08 (0.29), residues: 728
  helix: -1.74 (0.23), residues: 462
  sheet:  None (None), residues: 0
  loop : -2.37 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H 106 
 PHE   0.010   0.001   PHE E 104 
 TYR   0.019   0.002   TYR D 118 
 ARG   0.007   0.001   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06186 (  431)
  hydrogen bonds       : angle       3.03530 ( 1038)
  covalent geometry    : bond        0.00528 (12736)
  covalent geometry    : angle       0.63786 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7376 (tt0) cc_final: 0.6857 (tp30)
REVERT: B   31 LYS cc_start: 0.8593 (tttt) cc_final: 0.8338 (mptt)
REVERT: B   82 THR cc_start: 0.8477 (t) cc_final: 0.8115 (m)
REVERT: B   88 TYR cc_start: 0.8028 (m-10) cc_final: 0.7463 (m-10)
REVERT: C  101 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8745 (mp)
REVERT: D   48 ASP cc_start: 0.8167 (p0) cc_final: 0.7883 (p0)
REVERT: E   49 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.6082 (tpm170)
REVERT: F   84 MET cc_start: 0.6439 (mmm) cc_final: 0.5976 (mmm)
REVERT: F   88 TYR cc_start: 0.8398 (m-10) cc_final: 0.7729 (m-80)
REVERT: H   39 TYR cc_start: 0.8216 (t80) cc_final: 0.7787 (t80)
REVERT: H   80 TYR cc_start: 0.8051 (m-10) cc_final: 0.7560 (m-10)
  outliers start: 29
  outliers final: 23
  residues processed: 180
  average time/residue: 0.2912
  time to fit residues: 70.9152
Evaluate side-chains
  180 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue  121 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0060
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.135078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.112519 restraints weight = 24663.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.114350 restraints weight = 14574.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.115541 restraints weight = 10424.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12736  Z= 0.143
  Angle     :  0.553   9.198  18461  Z= 0.326
  Chirality :  0.033   0.140   2098
  Planarity :  0.004   0.049   1318
  Dihedral  : 30.019 158.195   4040
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.61 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 22.17 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.24 (0.30), residues: 728
  helix: -1.10 (0.24), residues: 468
  sheet:  None (None), residues: 0
  loop : -2.01 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H  46 
 PHE   0.007   0.001   PHE H  67 
 TYR   0.017   0.001   TYR D 118 
 ARG   0.006   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05317 (  431)
  hydrogen bonds       : angle       2.49647 ( 1038)
  covalent geometry    : bond        0.00312 (12736)
  covalent geometry    : angle       0.55348 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8967 (pt) cc_final: 0.8642 (mt)
REVERT: A   73 GLU cc_start: 0.7197 (tt0) cc_final: 0.6617 (tp30)
REVERT: B   59 LYS cc_start: 0.8397 (tttt) cc_final: 0.7748 (tmtt)
REVERT: B   72 TYR cc_start: 0.8712 (m-80) cc_final: 0.8471 (m-80)
REVERT: B   82 THR cc_start: 0.8437 (t) cc_final: 0.8078 (m)
REVERT: B   88 TYR cc_start: 0.7789 (m-10) cc_final: 0.7395 (m-10)
REVERT: D   48 ASP cc_start: 0.7974 (p0) cc_final: 0.7663 (p0)
REVERT: E   42 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.8002 (ttp80)
REVERT: F   84 MET cc_start: 0.6368 (mmm) cc_final: 0.4936 (tpp)
REVERT: F   88 TYR cc_start: 0.8312 (m-10) cc_final: 0.7507 (m-80)
REVERT: H   56 MET cc_start: 0.7737 (mmm) cc_final: 0.6902 (mtt)
REVERT: H   80 TYR cc_start: 0.7976 (m-10) cc_final: 0.7438 (m-10)
  outliers start: 17
  outliers final: 10
  residues processed: 174
  average time/residue: 0.2873
  time to fit residues: 67.1431
Evaluate side-chains
  155 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0970
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
F  25 ASN
G 103 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.133712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.110859 restraints weight = 25214.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112618 restraints weight = 15366.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.113786 restraints weight = 11186.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12736  Z= 0.160
  Angle     :  0.573   9.974  18461  Z= 0.333
  Chirality :  0.034   0.141   2098
  Planarity :  0.004   0.048   1318
  Dihedral  : 30.121 158.637   4040
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.71 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.30 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -1.98 (0.31), residues: 728
  helix: -0.88 (0.24), residues: 470
  sheet:  None (None), residues: 0
  loop : -1.95 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 106 
 PHE   0.006   0.001   PHE E 104 
 TYR   0.020   0.001   TYR D 118 
 ARG   0.005   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05393 (  431)
  hydrogen bonds       : angle       2.57920 ( 1038)
  covalent geometry    : bond        0.00359 (12736)
  covalent geometry    : angle       0.57342 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8984 (pt) cc_final: 0.8653 (mt)
REVERT: A   73 GLU cc_start: 0.7183 (tt0) cc_final: 0.6591 (tp30)
REVERT: B   72 TYR cc_start: 0.8747 (m-80) cc_final: 0.8532 (m-80)
REVERT: B   82 THR cc_start: 0.8460 (t) cc_final: 0.8084 (m)
REVERT: B   88 TYR cc_start: 0.7810 (m-10) cc_final: 0.7367 (m-10)
REVERT: D   48 ASP cc_start: 0.8067 (p0) cc_final: 0.7782 (p0)
REVERT: E   42 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.8115 (ttp80)
REVERT: F   25 ASN cc_start: 0.7802 (m-40) cc_final: 0.7368 (t0)
REVERT: F   84 MET cc_start: 0.6560 (mmm) cc_final: 0.5872 (mmm)
REVERT: F   88 TYR cc_start: 0.8376 (m-10) cc_final: 0.7726 (m-80)
REVERT: H   80 TYR cc_start: 0.7965 (m-10) cc_final: 0.7443 (m-10)
  outliers start: 16
  outliers final: 15
  residues processed: 156
  average time/residue: 0.2675
  time to fit residues: 56.8725
Evaluate side-chains
  153 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.130622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.106668 restraints weight = 24477.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.108350 restraints weight = 14991.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.109511 restraints weight = 11062.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12736  Z= 0.217
  Angle     :  0.625   9.979  18461  Z= 0.359
  Chirality :  0.037   0.155   2098
  Planarity :  0.004   0.049   1318
  Dihedral  : 30.431 159.471   4040
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.67 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 22.98 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.13 (0.30), residues: 728
  helix: -0.90 (0.24), residues: 472
  sheet:  None (None), residues: 0
  loop : -2.23 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 106 
 PHE   0.012   0.001   PHE H  67 
 TYR   0.028   0.002   TYR F  51 
 ARG   0.004   0.001   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06040 (  431)
  hydrogen bonds       : angle       2.87810 ( 1038)
  covalent geometry    : bond        0.00496 (12736)
  covalent geometry    : angle       0.62521 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8546 (mtp-110) cc_final: 0.7933 (mtp85)
REVERT: A   73 GLU cc_start: 0.7235 (tt0) cc_final: 0.6688 (tp30)
REVERT: B   59 LYS cc_start: 0.8459 (tttt) cc_final: 0.7966 (tmtt)
REVERT: B   82 THR cc_start: 0.8503 (t) cc_final: 0.8136 (m)
REVERT: B   88 TYR cc_start: 0.7914 (m-10) cc_final: 0.7383 (m-10)
REVERT: C   87 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7835 (mmt-90)
REVERT: D   48 ASP cc_start: 0.8183 (p0) cc_final: 0.7923 (p0)
REVERT: E   42 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8074 (ttp80)
REVERT: F   84 MET cc_start: 0.6619 (mmm) cc_final: 0.6065 (mmm)
REVERT: F   88 TYR cc_start: 0.8386 (m-10) cc_final: 0.7638 (m-80)
REVERT: H   80 TYR cc_start: 0.8014 (m-10) cc_final: 0.7515 (m-10)
  outliers start: 22
  outliers final: 18
  residues processed: 171
  average time/residue: 0.2818
  time to fit residues: 65.9564
Evaluate side-chains
  173 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   99 VAL
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.132890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.108807 restraints weight = 24127.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110610 restraints weight = 14741.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.111737 restraints weight = 10795.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12736  Z= 0.167
  Angle     :  0.582  10.236  18461  Z= 0.339
  Chirality :  0.034   0.145   2098
  Planarity :  0.004   0.050   1318
  Dihedral  : 30.213 158.427   4040
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.98 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.95 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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 (0.31), residues: 728
  helix: -0.60 (0.25), residues: 472
  sheet:  None (None), residues: 0
  loop : -2.04 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 106 
 PHE   0.014   0.001   PHE H  67 
 TYR   0.024   0.001   TYR D 118 
 ARG   0.004   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05522 (  431)
  hydrogen bonds       : angle       2.60190 ( 1038)
  covalent geometry    : bond        0.00376 (12736)
  covalent geometry    : angle       0.58185 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7127 (tt0) cc_final: 0.6669 (tp30)
REVERT: B   82 THR cc_start: 0.8482 (t) cc_final: 0.8091 (m)
REVERT: B   88 TYR cc_start: 0.7837 (m-10) cc_final: 0.7388 (m-10)
REVERT: C   87 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (mmt-90)
REVERT: D   48 ASP cc_start: 0.8132 (p0) cc_final: 0.7854 (p0)
REVERT: E   42 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.8064 (ttp80)
REVERT: F   84 MET cc_start: 0.6561 (mmm) cc_final: 0.5901 (mmm)
REVERT: F   88 TYR cc_start: 0.8358 (m-10) cc_final: 0.7701 (m-80)
REVERT: H   80 TYR cc_start: 0.8013 (m-10) cc_final: 0.7520 (m-10)
  outliers start: 25
  outliers final: 18
  residues processed: 174
  average time/residue: 0.2916
  time to fit residues: 68.9110
Evaluate side-chains
  172 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   99 VAL
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 92 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 96 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.134141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.110125 restraints weight = 24159.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.111898 restraints weight = 14840.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.113053 restraints weight = 10876.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12736  Z= 0.158
  Angle     :  0.574  10.217  18461  Z= 0.333
  Chirality :  0.034   0.142   2098
  Planarity :  0.004   0.050   1318
  Dihedral  : 30.132 157.067   4040
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.85 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.95 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.33 (0.32), residues: 728
  helix: -0.34 (0.25), residues: 466
  sheet:  None (None), residues: 0
  loop : -1.73 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS H 106 
 PHE   0.006   0.001   PHE A  78 
 TYR   0.025   0.002   TYR F  51 
 ARG   0.004   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05374 (  431)
  hydrogen bonds       : angle       2.55573 ( 1038)
  covalent geometry    : bond        0.00354 (12736)
  covalent geometry    : angle       0.57372 (18461)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7018 (tt0) cc_final: 0.6358 (tp30)
REVERT: B   82 THR cc_start: 0.8522 (t) cc_final: 0.8106 (m)
REVERT: B   88 TYR cc_start: 0.7835 (m-10) cc_final: 0.7362 (m-10)
REVERT: C   87 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7551 (mmt-90)
REVERT: D   48 ASP cc_start: 0.8126 (p0) cc_final: 0.7846 (p0)
REVERT: D   79 HIS cc_start: 0.8277 (t-90) cc_final: 0.8018 (t-90)
REVERT: E   42 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.8037 (ttp80)
REVERT: F   84 MET cc_start: 0.6511 (mmm) cc_final: 0.5755 (mmm)
REVERT: F   88 TYR cc_start: 0.8324 (m-10) cc_final: 0.7722 (m-80)
REVERT: G  103 GLN cc_start: 0.8521 (pt0) cc_final: 0.8228 (pt0)
REVERT: H   80 TYR cc_start: 0.7953 (m-10) cc_final: 0.7489 (m-10)
  outliers start: 23
  outliers final: 20
  residues processed: 167
  average time/residue: 0.3399
  time to fit residues: 78.2438
Evaluate side-chains
  168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   99 VAL
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0570
   chunk 75 optimal weight:    7.9990
   chunk 95 optimal weight:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.4902

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  93 ASN
G  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.133803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.109845 restraints weight = 24067.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111600 restraints weight = 14712.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.112753 restraints weight = 10825.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12736  Z= 0.168
  Angle     :  0.585   9.841  18461  Z= 0.339
  Chirality :  0.034   0.144   2098
  Planarity :  0.004   0.050   1318
  Dihedral  : 30.149 157.405   4040
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.71 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.95 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.22 (0.32), residues: 728
  helix: -0.27 (0.25), residues: 470
  sheet:  None (None), residues: 0
  loop : -1.67 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 106 
 PHE   0.016   0.001   PHE H  67 
 TYR   0.035   0.002   TYR F  51 
 ARG   0.004   0.000   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05440 (  431)
  hydrogen bonds       : angle       2.59270 ( 1038)
  covalent geometry    : bond        0.00380 (12736)
  covalent geometry    : angle       0.58451 (18461)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4913.08 seconds
wall clock time: 89 minutes 29.62 seconds (5369.62 seconds total)