Starting phenix.real_space_refine
on Tue Mar  3 23:16:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4h_30078/03_2026/6m4h_30078.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.005 sd=   0.063
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     206      5.49       5
     S      16      5.16       5
     C    5279      2.51       5
     N    1735      2.21       5
     O    2184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9420
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "I"
      Number of atoms: 2132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 2132
          Classifications: {'DNA': 103}
          Link IDs: {'rna3p': 102}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen planarities: 1
    Chain: "J"
      Number of atoms: 2090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 2090
          Classifications: {'DNA': 103}
          Link IDs: {'rna3p': 102}
    Chain: "A"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 599
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 610
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 1, 'TRANS': 74}
    Chain: "C"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 705
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "D"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 685
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
    Chain: "E"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 599
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "F"
      Number of atoms: 610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 610
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 1, 'TRANS': 74}
    Chain: "G"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 705
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "H"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 685
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
  Time building chain proxies: 1.99, per 1000 atoms: 0.21
  Number of scatterers: 9420
  At special positions: 0
  Unit cell: (97.76, 114.4, 113.36, 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      16     16.00
     P     206     15.00
     O    2184      8.00
     N    1735      7.00
     C    5279      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: 0.64
  Conformation dependent library (CDL) restraints added in 210.2 milliseconds
  

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      74.7% alpha, 2.1% beta
      98 base pairs and 164 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.585A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.532A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.628A  pdb=" N   GLY B  28 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.635A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.647A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 25
    Processing helix  chain 'C' and resid 30 through 40
    Processing helix  chain 'C' and resid 52 through 78
      removed outlier: 3.865A  pdb=" N   GLU C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C  69 " --> pdb=" O   LYS C  65 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN C  75 " --> pdb=" O   GLY C  71 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ASN C  76 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 93
      removed outlier: 3.786A  pdb=" N   HIS C  92 " --> pdb=" O   ASP C  88 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN C  93 " --> pdb=" O   MET C  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.703A  pdb=" N   TYR D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS D  43 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 84
      removed outlier: 3.608A  pdb=" N   GLY D  60 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY D  75 " --> pdb=" O   GLU D  71 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.689A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 4.028A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.583A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.532A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.628A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.634A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.648A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 21 through 25
    Processing helix  chain 'G' and resid 30 through 40
    Processing helix  chain 'G' and resid 50 through 76
      removed outlier: 3.865A  pdb=" N   GLU G  68 " --> pdb=" O   ALA G  64 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU G  69 " --> pdb=" O   LYS G  65 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN G  75 " --> pdb=" O   GLY G  71 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 83 through 93
      removed outlier: 3.788A  pdb=" N   HIS G  92 " --> pdb=" O   ASP G  88 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN G  93 " --> pdb=" O   MET G  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.702A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS H  43 " --> pdb=" O   ILE H  39 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 56 through 84
      removed outlier: 3.607A  pdb=" N   GLY H  60 " --> pdb=" O   SER H  56 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY H  75 " --> pdb=" O   GLU H  71 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.689A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 4.027A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.336A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 106
      removed outlier: 6.729A  pdb=" N   THR C 105 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.123A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119

    316 hydrogen bonds defined for protein.
    942 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      249 hydrogen bonds
      486 hydrogen bond angles
      0 basepair planarities
      98 basepair parallelities
      164 stacking parallelities
  Total time for adding SS restraints: 1.50

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1574
        1.33 -     1.45: 3361
        1.45 -     1.57: 4624
        1.57 -     1.69: 412
        1.69 -     1.80: 28
  Bond restraints: 9999
  Sorted by residual:
  bond pdb=" C   ARG G  49 "
       pdb=" N   THR G  50 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.046 1.27e-02 6.20e+03 1.33e+01
  bond pdb=" N   GLU G  79 "
       pdb=" CA  GLU G  79 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.27e-02 6.20e+03 1.01e+01
  bond pdb=" N   GLN C  75 "
       pdb=" CA  GLN C  75 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.034 1.16e-02 7.43e+03 8.37e+00
  bond pdb=" N   SER G  77 "
       pdb=" CA  SER G  77 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.25e-02 6.40e+03 7.31e+00
  bond pdb=" N   SER C  77 "
       pdb=" CA  SER C  77 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.10e+00
  ... (remaining 9994 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 14258
        3.12 -     6.24: 126
        6.24 -     9.36: 10
        9.36 -    12.48: 0
       12.48 -    15.60: 1
  Bond angle restraints: 14395
  Sorted by residual:
  angle pdb=" N   ASN G  76 "
        pdb=" CA  ASN G  76 "
        pdb=" C   ASN G  76 "
      ideal   model   delta    sigma   weight residual
     113.37  106.59    6.78 1.38e+00 5.25e-01 2.41e+01
  angle pdb=" C   ASN G  76 "
        pdb=" N   SER G  77 "
        pdb=" CA  SER G  77 "
      ideal   model   delta    sigma   weight residual
     121.87  129.48   -7.61 1.64e+00 3.72e-01 2.15e+01
  angle pdb=" CB  GLU F  53 "
        pdb=" CG  GLU F  53 "
        pdb=" CD  GLU F  53 "
      ideal   model   delta    sigma   weight residual
     112.60  119.77   -7.17 1.70e+00 3.46e-01 1.78e+01
  angle pdb=" CB  GLU B  53 "
        pdb=" CG  GLU B  53 "
        pdb=" CD  GLU B  53 "
      ideal   model   delta    sigma   weight residual
     112.60  119.71   -7.11 1.70e+00 3.46e-01 1.75e+01
  angle pdb=" C   CYS E  96 "
        pdb=" N   GLU E  97 "
        pdb=" CA  GLU E  97 "
      ideal   model   delta    sigma   weight residual
     120.68  113.87    6.81 1.70e+00 3.46e-01 1.60e+01
  ... (remaining 14390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.17: 4392
       35.17 -    70.34: 1018
       70.34 -   105.51: 46
      105.51 -   140.69: 4
      140.69 -   175.86: 6
  Dihedral angle restraints: 5466
    sinusoidal: 3548
      harmonic: 1918
  Sorted by residual:
  dihedral pdb=" C4'  DC I  34 "
           pdb=" C3'  DC I  34 "
           pdb=" O3'  DC I  34 "
           pdb=" P    DT I  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.86 -175.86     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J  32 "
           pdb=" C3'  DT J  32 "
           pdb=" O3'  DT J  32 "
           pdb=" P    DG J  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   32.37 -172.37     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  HIS G  92 "
           pdb=" C   HIS G  92 "
           pdb=" N   ASN G  93 "
           pdb=" CA  ASN G  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.29   19.71     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5463 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 962
       0.035 -    0.071: 491
       0.071 -    0.106: 156
       0.106 -    0.141: 45
       0.141 -    0.176: 12
  Chirality restraints: 1666
  Sorted by residual:
  chirality pdb=" CA  GLU A  97 "
            pdb=" N   GLU A  97 "
            pdb=" C   GLU A  97 "
            pdb=" CB  GLU A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.76e-01
  chirality pdb=" CA  GLU F  52 "
            pdb=" N   GLU F  52 "
            pdb=" C   GLU F  52 "
            pdb=" CB  GLU F  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  chirality pdb=" CA  GLU E  97 "
            pdb=" N   GLU E  97 "
            pdb=" C   GLU E  97 "
            pdb=" CB  GLU E  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.48e-01
  ... (remaining 1663 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  51 "   -0.099 5.00e-02 4.00e+02   1.53e-01 3.74e+01
        pdb=" N   PRO C  52 "    0.265 5.00e-02 4.00e+02
        pdb=" CA  PRO C  52 "   -0.090 5.00e-02 4.00e+02
        pdb=" CD  PRO C  52 "   -0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D  67 "    0.020 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        pdb=" C   ASN D  67 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   ASN D  67 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ASP D  68 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN H  67 "   -0.020 2.00e-02 2.50e+03   4.07e-02 1.66e+01
        pdb=" C   ASN H  67 "    0.070 2.00e-02 2.50e+03
        pdb=" O   ASN H  67 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ASP H  68 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 33
        2.36 -     3.00: 4572
        3.00 -     3.63: 17703
        3.63 -     4.27: 25383
        4.27 -     4.90: 36252
  Nonbonded interactions: 83943
  Sorted by model distance:
  nonbonded pdb=" OP1  DT J  31 "
            pdb=" OG  SER C  20 "
     model   vdw
     1.729 3.040
  nonbonded pdb=" OP1  DT J  31 "
            pdb=" CA  SER C  20 "
     model   vdw
     1.765 3.470
  nonbonded pdb=" OP2  DC I  81 "
            pdb=" N   GLY B  48 "
     model   vdw
     1.880 3.120
  nonbonded pdb=" OP2  DA J  91 "
            pdb=" NH2 ARG E  69 "
     model   vdw
     1.970 3.120
  nonbonded pdb=" OP2  DA I 113 "
            pdb=" NH2 ARG C  39 "
     model   vdw
     1.974 3.120
  ... (remaining 83938 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.000
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
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      :  0.008   0.056   9999  Z= 0.358
  Angle     :  0.894  15.598  14395  Z= 0.532
  Chirality :  0.048   0.176   1666
  Planarity :  0.010   0.153   1100
  Dihedral  : 29.217 175.856   4222
  Min Nonbonded Distance : 1.729

Molprobity Statistics.
  All-atom Clashscore : 27.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.12 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  :  2.31 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.02 (0.19), residues: 640
  helix: -4.08 (0.11), residues: 444
  sheet:  None (None), residues: 0
  loop : -3.15 (0.32), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  78 
 TYR   0.026   0.003   TYR B  51 
 PHE   0.021   0.003   PHE E  67 
 HIS   0.011   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00768 ( 9999)
  covalent geometry    : angle       0.89422 (14395)
  hydrogen bonds       : bond        0.13054 (  565)
  hydrogen bonds       : angle       5.08564 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 287
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8298 (m)
REVERT: B   59 LYS cc_start: 0.8613 (tttt) cc_final: 0.8119 (ttmt)
REVERT: B   75 HIS cc_start: 0.7843 (t-90) cc_final: 0.7516 (t-170)
REVERT: B   80 THR cc_start: 0.7724 (m) cc_final: 0.7488 (p)
REVERT: B   84 MET cc_start: 0.6505 (mmm) cc_final: 0.5995 (mmm)
REVERT: C   68 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: D   62 MET cc_start: 0.8518 (mmm) cc_final: 0.8317 (mmt)
REVERT: D   68 ASP cc_start: 0.7408 (t70) cc_final: 0.7073 (t0)
REVERT: D   70 PHE cc_start: 0.8359 (t80) cc_final: 0.8127 (t80)
REVERT: D  102 LEU cc_start: 0.8193 (mp) cc_final: 0.7980 (mp)
REVERT: E  101 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (m)
REVERT: F   29 ILE cc_start: 0.8916 (mm) cc_final: 0.8632 (mm)
REVERT: F   59 LYS cc_start: 0.8493 (tttt) cc_final: 0.8097 (tttp)
REVERT: F   75 HIS cc_start: 0.7852 (t-90) cc_final: 0.7429 (t70)
REVERT: G   31 VAL cc_start: 0.7902 (m) cc_final: 0.7430 (p)
REVERT: H   37 TYR cc_start: 0.5303 (m-10) cc_final: 0.4674 (m-80)
REVERT: H   62 MET cc_start: 0.8383 (mmm) cc_final: 0.8092 (mmt)
REVERT: H   68 ASP cc_start: 0.7535 (t70) cc_final: 0.7027 (t0)
  outliers start: 16
  outliers final: 2
  residues processed: 292
  average time/residue: 0.1465
  time to fit residues: 52.7622
Evaluate side-chains
  153 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain G residue   48 SER
Chi-restraints excluded: chain G residue  104 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  75 HIS
C  72 ASN
D  82 HIS
E  68 GLN
G  75 GLN
** G  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
H  95 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.047838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.036700 restraints weight = 65144.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.037858 restraints weight = 31060.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.038616 restraints weight = 19693.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.039054 restraints weight = 14828.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.039371 restraints weight = 12617.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9999  Z= 0.186
  Angle     :  0.717   9.935  14395  Z= 0.416
  Chirality :  0.040   0.156   1666
  Planarity :  0.007   0.057   1100
  Dihedral  : 33.515 171.093   2966
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.08 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.28), residues: 640
  helix: -1.48 (0.20), residues: 472
  sheet:  None (None), residues: 0
  loop : -2.44 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  92 
 TYR   0.017   0.002   TYR F  88 
 PHE   0.012   0.001   PHE A  78 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9999)
  covalent geometry    : angle       0.71718 (14395)
  hydrogen bonds       : bond        0.06625 (  565)
  hydrogen bonds       : angle       3.55113 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9036 (mt0) cc_final: 0.8626 (mt0)
REVERT: A   86 SER cc_start: 0.8962 (t) cc_final: 0.8486 (m)
REVERT: A  128 ARG cc_start: 0.9101 (mtp85) cc_final: 0.8777 (mtp85)
REVERT: B   59 LYS cc_start: 0.9211 (tttt) cc_final: 0.8739 (tptm)
REVERT: B   63 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8193 (mt-10)
REVERT: B   80 THR cc_start: 0.8858 (m) cc_final: 0.8432 (p)
REVERT: C   31 VAL cc_start: 0.8836 (m) cc_final: 0.8157 (p)
REVERT: C   33 GLN cc_start: 0.8929 (tt0) cc_final: 0.8184 (tm-30)
REVERT: C   68 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: C   72 ASN cc_start: 0.8332 (m-40) cc_final: 0.7885 (m-40)
REVERT: D   40 TYR cc_start: 0.8882 (m-80) cc_final: 0.8422 (m-80)
REVERT: D   93 GLU cc_start: 0.8447 (mp0) cc_final: 0.8114 (mm-30)
REVERT: D  101 LEU cc_start: 0.9079 (mm) cc_final: 0.8861 (mm)
REVERT: D  105 GLU cc_start: 0.8608 (pm20) cc_final: 0.8389 (pm20)
REVERT: E   85 GLN cc_start: 0.8967 (mt0) cc_final: 0.8582 (mt0)
REVERT: E   86 SER cc_start: 0.8971 (t) cc_final: 0.8512 (m)
REVERT: F   59 LYS cc_start: 0.9249 (tttt) cc_final: 0.8941 (tttp)
REVERT: F   75 HIS cc_start: 0.8579 (t-90) cc_final: 0.8248 (t-170)
REVERT: F   92 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8117 (tpp80)
REVERT: G   31 VAL cc_start: 0.8727 (m) cc_final: 0.8159 (p)
REVERT: G   68 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: H   93 GLU cc_start: 0.8547 (mp0) cc_final: 0.8123 (mm-30)
  outliers start: 21
  outliers final: 9
  residues processed: 198
  average time/residue: 0.1222
  time to fit residues: 31.0232
Evaluate side-chains
  164 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   95 GLN
Chi-restraints excluded: chain H residue   99 ARG
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  49 HIS
D  84 ASN
E  93 GLN
G  45 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.045873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.034742 restraints weight = 66286.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.035820 restraints weight = 32802.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.036489 restraints weight = 21211.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.036947 restraints weight = 16364.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037178 restraints weight = 13947.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9999  Z= 0.250
  Angle     :  0.729   6.658  14395  Z= 0.421
  Chirality :  0.041   0.178   1666
  Planarity :  0.005   0.047   1100
  Dihedral  : 33.439 173.672   2962
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.11 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.31), residues: 640
  helix:  0.12 (0.22), residues: 484
  sheet:  None (None), residues: 0
  loop : -2.39 (0.42), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  92 
 TYR   0.019   0.002   TYR C  61 
 PHE   0.006   0.001   PHE E  84 
 HIS   0.010   0.002   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 9999)
  covalent geometry    : angle       0.72891 (14395)
  hydrogen bonds       : bond        0.06839 (  565)
  hydrogen bonds       : angle       3.44784 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 SER cc_start: 0.9167 (t) cc_final: 0.8732 (m)
REVERT: A   90 MET cc_start: 0.9034 (mmm) cc_final: 0.8545 (mmp)
REVERT: B   59 LYS cc_start: 0.9258 (tttt) cc_final: 0.8833 (tptm)
REVERT: B   63 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: B   80 THR cc_start: 0.9051 (m) cc_final: 0.8597 (p)
REVERT: C   31 VAL cc_start: 0.9141 (m) cc_final: 0.8658 (p)
REVERT: C   33 GLN cc_start: 0.9018 (tt0) cc_final: 0.8302 (tm-30)
REVERT: C   68 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8043 (tm-30)
REVERT: C   76 ASN cc_start: 0.8951 (p0) cc_final: 0.8470 (p0)
REVERT: C   80 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6981 (tpp-160)
REVERT: D   93 GLU cc_start: 0.8643 (mp0) cc_final: 0.8402 (mm-30)
REVERT: E   68 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8411 (tp-100)
REVERT: E   86 SER cc_start: 0.9098 (t) cc_final: 0.8757 (m)
REVERT: E   90 MET cc_start: 0.9014 (mmm) cc_final: 0.8737 (mmp)
REVERT: F   84 MET cc_start: 0.8554 (tpp) cc_final: 0.8305 (tpp)
REVERT: F   88 TYR cc_start: 0.9006 (m-80) cc_final: 0.8765 (m-80)
REVERT: G   31 VAL cc_start: 0.9206 (m) cc_final: 0.8929 (p)
REVERT: G   60 GLU cc_start: 0.9068 (tt0) cc_final: 0.7923 (tt0)
REVERT: H   93 GLU cc_start: 0.8595 (mp0) cc_final: 0.8282 (mm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 171
  average time/residue: 0.1232
  time to fit residues: 27.1827
Evaluate side-chains
  143 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   59 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 66 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:   30.0000
   chunk 52 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    2.6784

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

Flipped N/Q/H residues before XYZ refinement:
C  75 GLN
** D  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.045709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.034602 restraints weight = 66304.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.035654 restraints weight = 32160.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.036343 restraints weight = 20718.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.036740 restraints weight = 15850.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.037010 restraints weight = 13614.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9999  Z= 0.226
  Angle     :  0.698   5.603  14395  Z= 0.405
  Chirality :  0.040   0.173   1666
  Planarity :  0.005   0.043   1100
  Dihedral  : 33.375 174.990   2962
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.53 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.33), residues: 640
  helix:  0.82 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.14 (0.44), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  92 
 TYR   0.020   0.002   TYR G  61 
 PHE   0.007   0.001   PHE D  70 
 HIS   0.019   0.002   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 9999)
  covalent geometry    : angle       0.69819 (14395)
  hydrogen bonds       : bond        0.06506 (  565)
  hydrogen bonds       : angle       3.32772 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9061 (mmm) cc_final: 0.8669 (mmp)
REVERT: B   80 THR cc_start: 0.9070 (m) cc_final: 0.8713 (p)
REVERT: C   31 VAL cc_start: 0.9278 (m) cc_final: 0.8760 (p)
REVERT: C   33 GLN cc_start: 0.9050 (tt0) cc_final: 0.8593 (tm-30)
REVERT: C   61 TYR cc_start: 0.8550 (t80) cc_final: 0.8067 (t80)
REVERT: C   68 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8147 (tm-30)
REVERT: D   99 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8126 (mpp80)
REVERT: E   90 MET cc_start: 0.9009 (mmm) cc_final: 0.8656 (mmp)
REVERT: E  125 GLN cc_start: 0.9128 (mt0) cc_final: 0.8863 (mt0)
REVERT: F   84 MET cc_start: 0.8653 (tpp) cc_final: 0.8226 (tpp)
REVERT: F   88 TYR cc_start: 0.9015 (m-80) cc_final: 0.8693 (m-80)
REVERT: G   31 VAL cc_start: 0.9347 (m) cc_final: 0.9105 (p)
REVERT: G   60 GLU cc_start: 0.9186 (tt0) cc_final: 0.7912 (tt0)
  outliers start: 21
  outliers final: 14
  residues processed: 165
  average time/residue: 0.1175
  time to fit residues: 25.0909
Evaluate side-chains
  154 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** C  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 HIS
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.046376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.035309 restraints weight = 66624.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.036377 restraints weight = 32745.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.037069 restraints weight = 21163.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.037505 restraints weight = 16219.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.037771 restraints weight = 13813.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9999  Z= 0.180
  Angle     :  0.676  10.099  14395  Z= 0.387
  Chirality :  0.038   0.163   1666
  Planarity :  0.004   0.039   1100
  Dihedral  : 33.205 179.326   2962
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.49 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.33), residues: 640
  helix:  1.29 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -1.81 (0.45), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  92 
 TYR   0.042   0.002   TYR B  88 
 PHE   0.007   0.001   PHE A  78 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 9999)
  covalent geometry    : angle       0.67619 (14395)
  hydrogen bonds       : bond        0.06061 (  565)
  hydrogen bonds       : angle       3.12033 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9075 (mmm) cc_final: 0.8662 (mmp)
REVERT: A  128 ARG cc_start: 0.9183 (mtp85) cc_final: 0.8878 (mtp85)
REVERT: B   75 HIS cc_start: 0.8694 (t70) cc_final: 0.8274 (t-170)
REVERT: B   80 THR cc_start: 0.9069 (m) cc_final: 0.8709 (p)
REVERT: B   84 MET cc_start: 0.8563 (tpp) cc_final: 0.8336 (tpp)
REVERT: C   31 VAL cc_start: 0.9191 (m) cc_final: 0.8608 (p)
REVERT: C   33 GLN cc_start: 0.9045 (tt0) cc_final: 0.8592 (tm-30)
REVERT: C   68 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: D   40 TYR cc_start: 0.8690 (m-80) cc_final: 0.8337 (m-80)
REVERT: D   93 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7202 (tp30)
REVERT: D   99 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (mtm180)
REVERT: E   90 MET cc_start: 0.8989 (mmm) cc_final: 0.8626 (mmp)
REVERT: E  125 GLN cc_start: 0.9153 (mt0) cc_final: 0.8923 (mt0)
REVERT: F   59 LYS cc_start: 0.9316 (tttt) cc_final: 0.9049 (tttp)
REVERT: G   31 VAL cc_start: 0.9327 (m) cc_final: 0.8893 (p)
REVERT: G   60 GLU cc_start: 0.9101 (tt0) cc_final: 0.7807 (tt0)
REVERT: G   68 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8043 (pp20)
REVERT: H   99 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7917 (mpp80)
  outliers start: 15
  outliers final: 11
  residues processed: 156
  average time/residue: 0.1104
  time to fit residues: 22.7244
Evaluate side-chains
  144 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   95 GLN
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
E 113 HIS
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.045162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.034077 restraints weight = 66909.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.035117 restraints weight = 32901.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.035795 restraints weight = 21286.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036232 restraints weight = 16305.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.036474 restraints weight = 13859.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9999  Z= 0.247
  Angle     :  0.704   8.162  14395  Z= 0.403
  Chirality :  0.040   0.179   1666
  Planarity :  0.005   0.042   1100
  Dihedral  : 33.193 178.470   2962
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 24.02 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.33), residues: 640
  helix:  1.41 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -1.76 (0.46), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  46 
 TYR   0.019   0.002   TYR G  61 
 PHE   0.017   0.001   PHE H  70 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9999)
  covalent geometry    : angle       0.70373 (14395)
  hydrogen bonds       : bond        0.06531 (  565)
  hydrogen bonds       : angle       3.32832 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9065 (mmm) cc_final: 0.8652 (mmp)
REVERT: A  125 GLN cc_start: 0.9141 (mt0) cc_final: 0.8871 (mt0)
REVERT: B   75 HIS cc_start: 0.8659 (t70) cc_final: 0.8428 (t-170)
REVERT: B   80 THR cc_start: 0.9216 (m) cc_final: 0.8912 (p)
REVERT: B   88 TYR cc_start: 0.9111 (m-80) cc_final: 0.8910 (m-80)
REVERT: C   33 GLN cc_start: 0.9067 (tt0) cc_final: 0.8625 (tm-30)
REVERT: C   68 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: D   99 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7769 (mpp80)
REVERT: E   68 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8491 (tp-100)
REVERT: E   90 MET cc_start: 0.8987 (mmm) cc_final: 0.8618 (mmp)
REVERT: E  125 GLN cc_start: 0.9115 (mt0) cc_final: 0.8851 (mt0)
REVERT: F   59 LYS cc_start: 0.9336 (tttt) cc_final: 0.9070 (tttp)
REVERT: G   31 VAL cc_start: 0.9437 (m) cc_final: 0.9051 (p)
REVERT: G   60 GLU cc_start: 0.9183 (tt0) cc_final: 0.8016 (tt0)
REVERT: H   61 ILE cc_start: 0.9170 (mm) cc_final: 0.8966 (mm)
REVERT: H   99 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8055 (mpp80)
  outliers start: 20
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1225
  time to fit residues: 23.0653
Evaluate side-chains
  138 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 VAL
Chi-restraints excluded: chain G residue   59 ILE
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0370
   chunk 72 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.047164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.036118 restraints weight = 66135.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.037172 restraints weight = 32011.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.037885 restraints weight = 20589.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.038314 restraints weight = 15695.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.038618 restraints weight = 13392.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9999  Z= 0.162
  Angle     :  0.654   8.239  14395  Z= 0.378
  Chirality :  0.038   0.179   1666
  Planarity :  0.004   0.040   1100
  Dihedral  : 32.922 177.627   2962
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 24.56 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.33), residues: 640
  helix:  1.80 (0.24), residues: 476
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 128 
 TYR   0.022   0.002   TYR H  40 
 PHE   0.007   0.001   PHE E  78 
 HIS   0.002   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9999)
  covalent geometry    : angle       0.65422 (14395)
  hydrogen bonds       : bond        0.05909 (  565)
  hydrogen bonds       : angle       3.18254 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9047 (mmm) cc_final: 0.8625 (mmp)
REVERT: A  125 GLN cc_start: 0.9154 (mt0) cc_final: 0.8946 (mt0)
REVERT: B   80 THR cc_start: 0.9095 (m) cc_final: 0.8739 (p)
REVERT: B   84 MET cc_start: 0.8827 (tpp) cc_final: 0.8597 (tpp)
REVERT: C   31 VAL cc_start: 0.9253 (m) cc_final: 0.8666 (p)
REVERT: C   33 GLN cc_start: 0.9028 (tt0) cc_final: 0.8588 (tm-30)
REVERT: C   42 HIS cc_start: 0.8755 (m90) cc_final: 0.8460 (m90)
REVERT: C   68 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: D   40 TYR cc_start: 0.8556 (m-80) cc_final: 0.8197 (m-80)
REVERT: D   93 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7129 (tp30)
REVERT: D   99 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7717 (mtm-85)
REVERT: E   90 MET cc_start: 0.8921 (mmm) cc_final: 0.8494 (mmp)
REVERT: F   59 LYS cc_start: 0.9284 (tttt) cc_final: 0.9022 (tttp)
REVERT: G   31 VAL cc_start: 0.9331 (m) cc_final: 0.8878 (p)
REVERT: G   60 GLU cc_start: 0.9106 (tt0) cc_final: 0.7951 (tt0)
REVERT: G   68 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8069 (pp20)
REVERT: H   61 ILE cc_start: 0.9113 (mm) cc_final: 0.8906 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 152
  average time/residue: 0.1164
  time to fit residues: 23.5218
Evaluate side-chains
  141 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   64 SER
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   90 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.046049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.034883 restraints weight = 66005.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.035911 restraints weight = 32614.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.036568 restraints weight = 21216.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.037013 restraints weight = 16393.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.037261 restraints weight = 13967.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.5487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9999  Z= 0.219
  Angle     :  0.681   7.234  14395  Z= 0.391
  Chirality :  0.039   0.178   1666
  Planarity :  0.005   0.040   1100
  Dihedral  : 32.976 177.677   2962
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 25.62 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.33), residues: 640
  helix:  1.77 (0.23), residues: 480
  sheet:  None (None), residues: 0
  loop : -1.78 (0.42), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  80 
 TYR   0.045   0.003   TYR B  88 
 PHE   0.005   0.001   PHE B 100 
 HIS   0.012   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 9999)
  covalent geometry    : angle       0.68135 (14395)
  hydrogen bonds       : bond        0.06273 (  565)
  hydrogen bonds       : angle       3.37104 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9034 (mmm) cc_final: 0.8597 (mmp)
REVERT: B   80 THR cc_start: 0.9230 (m) cc_final: 0.8878 (p)
REVERT: C   33 GLN cc_start: 0.9057 (tt0) cc_final: 0.8682 (tm-30)
REVERT: C   40 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8300 (mt-10)
REVERT: C   42 HIS cc_start: 0.8754 (m90) cc_final: 0.8401 (m90)
REVERT: C   68 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8220 (tm-30)
REVERT: D   93 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7148 (tp30)
REVERT: D   99 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7849 (ttm170)
REVERT: E   90 MET cc_start: 0.8951 (mmm) cc_final: 0.8557 (mmp)
REVERT: F   59 LYS cc_start: 0.9322 (tttt) cc_final: 0.9081 (tttp)
REVERT: G   31 VAL cc_start: 0.9377 (m) cc_final: 0.8932 (p)
REVERT: G   60 GLU cc_start: 0.9155 (tt0) cc_final: 0.8032 (tt0)
  outliers start: 15
  outliers final: 12
  residues processed: 137
  average time/residue: 0.1181
  time to fit residues: 21.4399
Evaluate side-chains
  135 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 VAL
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   95 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
H  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.047309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.036159 restraints weight = 66534.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.037202 restraints weight = 33226.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.037899 restraints weight = 21635.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.038319 restraints weight = 16606.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.038613 restraints weight = 14246.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.5769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9999  Z= 0.166
  Angle     :  0.668   7.245  14395  Z= 0.384
  Chirality :  0.038   0.149   1666
  Planarity :  0.004   0.040   1100
  Dihedral  : 32.812 176.354   2962
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 25.98 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.33), residues: 640
  helix:  1.73 (0.24), residues: 480
  sheet:  None (None), residues: 0
  loop : -1.64 (0.42), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 128 
 TYR   0.024   0.002   TYR H  83 
 PHE   0.019   0.001   PHE H  70 
 HIS   0.010   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9999)
  covalent geometry    : angle       0.66751 (14395)
  hydrogen bonds       : bond        0.05911 (  565)
  hydrogen bonds       : angle       3.33462 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8969 (mmm) cc_final: 0.8584 (mmp)
REVERT: B   80 THR cc_start: 0.9170 (m) cc_final: 0.8838 (p)
REVERT: C   31 VAL cc_start: 0.9320 (m) cc_final: 0.8759 (p)
REVERT: C   33 GLN cc_start: 0.9029 (tt0) cc_final: 0.8594 (tm-30)
REVERT: C   42 HIS cc_start: 0.8671 (m90) cc_final: 0.8397 (m90)
REVERT: C   68 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: D   40 TYR cc_start: 0.8523 (m-80) cc_final: 0.8200 (m-80)
REVERT: E   90 MET cc_start: 0.8871 (mmm) cc_final: 0.8458 (mmp)
REVERT: F   59 LYS cc_start: 0.9295 (tttt) cc_final: 0.9049 (tttp)
REVERT: F   84 MET cc_start: 0.8553 (tpp) cc_final: 0.8280 (tpp)
REVERT: G   31 VAL cc_start: 0.9272 (m) cc_final: 0.8796 (p)
REVERT: G   60 GLU cc_start: 0.9100 (tt0) cc_final: 0.8009 (tt0)
  outliers start: 13
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1078
  time to fit residues: 20.5368
Evaluate side-chains
  136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 VAL
Chi-restraints excluded: chain H residue   69 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 75 optimal weight:    0.0000
   chunk 29 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  75 GLN
H  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.046756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.035479 restraints weight = 66478.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.036501 restraints weight = 33714.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.037191 restraints weight = 22166.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.037610 restraints weight = 17116.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.037849 restraints weight = 14694.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9999  Z= 0.196
  Angle     :  0.689   7.944  14395  Z= 0.393
  Chirality :  0.039   0.157   1666
  Planarity :  0.005   0.066   1100
  Dihedral  : 32.795 175.551   2962
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.80 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.33), residues: 640
  helix:  1.70 (0.23), residues: 480
  sheet:  None (None), residues: 0
  loop : -1.50 (0.43), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  80 
 TYR   0.042   0.002   TYR B  88 
 PHE   0.006   0.001   PHE B 100 
 HIS   0.009   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 9999)
  covalent geometry    : angle       0.68925 (14395)
  hydrogen bonds       : bond        0.06037 (  565)
  hydrogen bonds       : angle       3.43040 ( 1428)

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

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

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1280 Ramachandran restraints generated.
    640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   90 MET cc_start: 0.9003 (mmm) cc_final: 0.8570 (mmp)
REVERT: B   80 THR cc_start: 0.9239 (m) cc_final: 0.8893 (p)
REVERT: C   31 VAL cc_start: 0.9353 (m) cc_final: 0.8830 (p)
REVERT: C   33 GLN cc_start: 0.9047 (tt0) cc_final: 0.8832 (tm-30)
REVERT: C   42 HIS cc_start: 0.8662 (m90) cc_final: 0.8414 (m90)
REVERT: C   68 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: D   37 TYR cc_start: 0.7898 (m-80) cc_final: 0.7606 (m-80)
REVERT: D   40 TYR cc_start: 0.8572 (m-80) cc_final: 0.8212 (m-80)
REVERT: D   71 GLU cc_start: 0.8759 (tt0) cc_final: 0.7956 (tm-30)
REVERT: D   99 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8037 (mtm180)
REVERT: E   90 MET cc_start: 0.8884 (mmm) cc_final: 0.8489 (mmp)
REVERT: F   59 LYS cc_start: 0.9305 (tttt) cc_final: 0.9064 (tttp)
REVERT: F   84 MET cc_start: 0.8601 (tpp) cc_final: 0.8337 (tpp)
REVERT: G   31 VAL cc_start: 0.9314 (m) cc_final: 0.8851 (p)
REVERT: G   60 GLU cc_start: 0.9124 (tt0) cc_final: 0.8054 (tt0)
REVERT: H   61 ILE cc_start: 0.9138 (mm) cc_final: 0.8917 (mm)
  outliers start: 16
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1213
  time to fit residues: 21.0140
Evaluate side-chains
  136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   99 ARG
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   23 VAL
Chi-restraints excluded: chain G residue   75 GLN
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   95 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 22 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.047698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.036498 restraints weight = 64981.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037557 restraints weight = 32280.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.038267 restraints weight = 20912.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.038692 restraints weight = 16000.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.038975 restraints weight = 13675.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.6030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9999  Z= 0.168
  Angle     :  0.682   8.196  14395  Z= 0.388
  Chirality :  0.038   0.148   1666
  Planarity :  0.005   0.059   1100
  Dihedral  : 32.695 174.405   2962
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 26.51 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.33), residues: 640
  helix:  1.68 (0.24), residues: 480
  sheet:  None (None), residues: 0
  loop : -1.41 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  80 
 TYR   0.018   0.002   TYR G  61 
 PHE   0.019   0.001   PHE H  70 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9999)
  covalent geometry    : angle       0.68214 (14395)
  hydrogen bonds       : bond        0.05916 (  565)
  hydrogen bonds       : angle       3.39478 ( 1428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.47 seconds
wall clock time: 26 minutes 27.89 seconds (1587.89 seconds total)