Starting phenix.real_space_refine
on Wed Mar  4 03:30:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x5a_33013/03_2026/7x5a_33013.cif"
  }
  resolution = 3.01
  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=  -0.000 sd=   0.078
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     104      5.49       5
     S      32      5.16       5
     C    6510      2.51       5
     N    1888      2.21       5
     O    2152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  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: 10686
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "I"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 26, 535
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "J"
      Number of atoms: 532
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 26, 532
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "K"
      Number of atoms: 533
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 26, 533
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "L"
      Number of atoms: 532
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 26, 532
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "A"
      Number of atoms: 1083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1083
          Classifications: {'peptide': 137}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 129}
    Chain: "B"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
    Chain: "C"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
    Chain: "D"
      Number of atoms: 1075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1075
          Classifications: {'peptide': 136}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128}
    Chain: "E"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
    Chain: "F"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
    Chain: "G"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
    Chain: "H"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1066
          Classifications: {'peptide': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" P  A DT I  36 " occ=0.25
      ... (18 atoms not shown)
      pdb=" C6 A DT I  36 " occ=0.25
    residue:
      pdb=" P  A DA I  42 " occ=0.25
      ... (19 atoms not shown)
      pdb=" C4 A DA I  42 " occ=0.25
    residue:
      pdb=" P  A DA K  20 " occ=0.25
      ... (19 atoms not shown)
      pdb=" C4 A DA K  20 " occ=0.25
    residue:
      pdb=" P  A DT K  26 " occ=0.25
      ... (18 atoms not shown)
      pdb=" C6 A DT K  26 " occ=0.25
  Time building chain proxies: 2.51, per 1000 atoms: 0.23
  Number of scatterers: 10686
  At special positions: 0
  Unit cell: (98.77, 112.88, 121.18, 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      32     16.00
     P     104     15.00
     O    2152      8.00
     N    1888      7.00
     C    6510      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: 0.87
  Conformation dependent library (CDL) restraints added in 439.6 milliseconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 2 sheets defined
      47.6% alpha, 11.8% beta
      36 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 65 through 77
    Processing helix  chain 'A' and resid 82 through 93
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 4.209A  pdb=" N   LEU A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'B' and resid 31 through 37
      removed outlier: 3.570A  pdb=" N   ARG B  37 " --> pdb=" O   THR B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 77
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'B' and resid 94 through 105
    Processing helix  chain 'B' and resid 107 through 112
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'C' and resid 31 through 36
    Processing helix  chain 'C' and resid 65 through 77
    Processing helix  chain 'C' and resid 82 through 93
    Processing helix  chain 'C' and resid 94 through 105
    Processing helix  chain 'C' and resid 106 through 113
      removed outlier: 4.032A  pdb=" N   LEU C 110 " --> pdb=" O   ASP C 106 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE C 113 " --> pdb=" O   THR C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 129
    Processing helix  chain 'D' and resid 31 through 36
    Processing helix  chain 'D' and resid 65 through 78
      removed outlier: 3.605A  pdb=" N   LEU D  78 " --> pdb=" O   GLU D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 93
    Processing helix  chain 'D' and resid 94 through 105
    Processing helix  chain 'D' and resid 107 through 112
      removed outlier: 3.607A  pdb=" N   LYS D 112 " --> pdb=" O   SER D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 132
      removed outlier: 4.088A  pdb=" N   ASP D 130 " --> pdb=" O   VAL D 126 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE D 132 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 31 through 36
    Processing helix  chain 'E' and resid 65 through 77
    Processing helix  chain 'E' and resid 82 through 93
    Processing helix  chain 'E' and resid 94 through 105
    Processing helix  chain 'E' and resid 106 through 113
      removed outlier: 3.868A  pdb=" N   LEU E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE E 113 " --> pdb=" O   THR E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 132
      removed outlier: 4.122A  pdb=" N   ASP E 130 " --> pdb=" O   VAL E 126 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 36
    Processing helix  chain 'F' and resid 65 through 77
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'F' and resid 94 through 105
    Processing helix  chain 'F' and resid 107 through 113
      removed outlier: 3.871A  pdb=" N   ILE F 113 " --> pdb=" O   THR F 109 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 117 through 128
      removed outlier: 3.562A  pdb=" N   ALA F 121 " --> pdb=" O   GLY F 117 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 31 through 37
      removed outlier: 3.701A  pdb=" N   ARG G  37 " --> pdb=" O   THR G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 65 through 77
    Processing helix  chain 'G' and resid 82 through 93
    Processing helix  chain 'G' and resid 94 through 105
    Processing helix  chain 'G' and resid 106 through 113
      removed outlier: 4.124A  pdb=" N   LEU G 110 " --> pdb=" O   ASP G 106 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE G 113 " --> pdb=" O   THR G 109 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 117 through 129
    Processing helix  chain 'H' and resid 31 through 36
    Processing helix  chain 'H' and resid 65 through 77
    Processing helix  chain 'H' and resid 82 through 93
    Processing helix  chain 'H' and resid 94 through 105
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.501A  pdb=" N   LYS H 112 " --> pdb=" O   SER H 108 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 117 through 132
      removed outlier: 3.871A  pdb=" N   ASP H 130 " --> pdb=" O   VAL H 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13
      removed outlier: 6.766A  pdb=" N   ILE A  18 " --> pdb=" O   ALA A  10 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   LYS A  12 " --> pdb=" O   HIS A  16 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   HIS A  16 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 24 through 29
    current: chain 'A' and resid 58 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 58 through 61
    current: chain 'B' and resid 16 through 21
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 24 through 29
    current: chain 'B' and resid 58 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 58 through 61
    current: chain 'C' and resid 16 through 21
      removed outlier: 3.507A  pdb=" N   VAL C  24 " --> pdb=" O   VAL C  21 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 24 through 29
    current: chain 'C' and resid 58 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 58 through 61
    current: chain 'D' and resid 16 through 21
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 24 through 29
    current: chain 'D' and resid 58 through 61
    Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 13
      removed outlier: 3.628A  pdb=" N   THR E   8 " --> pdb=" O   ASP E  20 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE E  18 " --> pdb=" O   ALA E  10 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LYS E  12 " --> pdb=" O   HIS E  16 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   HIS E  16 " --> pdb=" O   LYS E  12 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 24 through 29
    current: chain 'E' and resid 58 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 58 through 61
    current: chain 'F' and resid 16 through 21
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 24 through 29
    current: chain 'F' and resid 57 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 57 through 61
    current: chain 'G' and resid 16 through 21
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 24 through 29
    current: chain 'G' and resid 58 through 61
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 58 through 61
    current: chain 'H' and resid 16 through 21
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 24 through 29
    current: chain 'H' and resid 57 through 61

    356 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      144 hydrogen bond angles
      0 basepair planarities
      36 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2914
        1.34 -     1.45: 2025
        1.45 -     1.57: 5887
        1.57 -     1.69: 204
        1.69 -     1.81: 56
  Bond restraints: 11086
  Sorted by residual:
  bond pdb=" N9   DA K  11 "
       pdb=" C1'A DA K  11 "
    ideal  model  delta    sigma   weight residual
    1.460  1.502 -0.042 2.00e-02 2.50e+03 4.41e+00
  bond pdb=" N9   DA K  13 "
       pdb=" C1'A DA K  13 "
    ideal  model  delta    sigma   weight residual
    1.460  1.502 -0.042 2.00e-02 2.50e+03 4.31e+00
  bond pdb=" N9   DA K  27 "
       pdb=" C1'A DA K  27 "
    ideal  model  delta    sigma   weight residual
    1.460  1.501 -0.041 2.00e-02 2.50e+03 4.27e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" N   MET G   1 "
       pdb=" CA  MET G   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  ... (remaining 11081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.84: 14129
        0.84 -     1.68: 970
        1.68 -     2.52: 256
        2.52 -     3.35: 58
        3.35 -     4.19: 26
  Bond angle restraints: 15439
  Sorted by residual:
  angle pdb=" C3'A DA K  13 "
        pdb=" C2'A DA K  13 "
        pdb=" C1'A DA K  13 "
      ideal   model   delta    sigma   weight residual
     101.60  105.61   -4.01 1.50e+00 4.44e-01 7.15e+00
  angle pdb=" C3'A DA J  25 "
        pdb=" C2'A DA J  25 "
        pdb=" C1'A DA J  25 "
      ideal   model   delta    sigma   weight residual
     101.60  105.55   -3.95 1.50e+00 4.44e-01 6.93e+00
  angle pdb=" C4'A DA K  13 "
        pdb=" C3'A DA K  13 "
        pdb=" O3'A DA K  13 "
      ideal   model   delta    sigma   weight residual
     110.00  113.65   -3.65 1.50e+00 4.44e-01 5.91e+00
  angle pdb=" C3'A DA J  32 "
        pdb=" C2'A DA J  32 "
        pdb=" C1'A DA J  32 "
      ideal   model   delta    sigma   weight residual
     101.60  105.13   -3.53 1.50e+00 4.44e-01 5.54e+00
  angle pdb=" C4 A DT K  26 "
        pdb=" C5 A DT K  26 "
        pdb=" C7 A DT K  26 "
      ideal   model   delta    sigma   weight residual
     122.40  118.94    3.46 1.50e+00 4.44e-01 5.31e+00
  ... (remaining 15434 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.37: 5939
       31.37 -    62.74: 613
       62.74 -    94.10: 18
       94.10 -   125.47: 1
      125.47 -   156.84: 2
  Dihedral angle restraints: 6573
    sinusoidal: 3484
      harmonic: 3089
  Sorted by residual:
  dihedral pdb=" C4'A DA I  20 "
           pdb=" C3'A DA I  20 "
           pdb=" O3'A DA I  20 "
           pdb=" P  A DA I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.16  156.84     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" C4'A DT L  44 "
           pdb=" C3'A DT L  44 "
           pdb=" O3'A DT L  44 "
           pdb=" P  A DT L  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   65.27  154.73     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  LYS F 129 "
           pdb=" C   LYS F 129 "
           pdb=" N   ASP F 130 "
           pdb=" CA  ASP F 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.89  -17.11     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 6570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1156
       0.028 -    0.056: 404
       0.056 -    0.083: 116
       0.083 -    0.111: 84
       0.111 -    0.139: 43
  Chirality restraints: 1803
  Sorted by residual:
  chirality pdb=" CA  ILE B 113 "
            pdb=" N   ILE B 113 "
            pdb=" C   ILE B 113 "
            pdb=" CB  ILE B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE D 113 "
            pdb=" N   ILE D 113 "
            pdb=" C   ILE D 113 "
            pdb=" CB  ILE D 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE E 113 "
            pdb=" N   ILE E 113 "
            pdb=" C   ILE E 113 "
            pdb=" CB  ILE E 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  ... (remaining 1800 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  38 "    0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO D  39 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO D  39 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D  39 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 113 "    0.021 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO F 114 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO F 114 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO F 114 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 118 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   LYS C 118 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   LYS C 118 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LYS C 119 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 547
        2.73 -     3.27: 9924
        3.27 -     3.81: 18441
        3.81 -     4.36: 22135
        4.36 -     4.90: 36510
  Nonbonded interactions: 87557
  Sorted by model distance:
  nonbonded pdb=" O   LYS H 118 "
            pdb=" OE1 GLU H 122 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   VAL C 126 "
            pdb=" NZ  LYS G 119 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OP1A DA K  30 "
            pdb=" OG1 THR A 120 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG E 123 "
            pdb=" OE1 GLU E 127 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   LYS H 118 "
            pdb=" N   ALA H 121 "
     model   vdw
     2.248 3.120
  ... (remaining 87552 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' and resid 1 through 135)
  selection = chain 'B'
  selection = chain 'C'
  selection = (chain 'D' and resid 1 through 135)
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'K' and (resid 12 through 22 or resid 24 through 30 or resid 32 through 3 \ 
6))
  selection = (chain 'L' and (resid 21 through 24 or resid 26 through 32 or resid 34 through 4 \ 
5))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=0.92
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             11.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.100
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11086  Z= 0.133
  Angle     :  0.534   4.193  15439  Z= 0.310
  Chirality :  0.040   0.139   1803
  Planarity :  0.003   0.052   1598
  Dihedral  : 20.334 156.839   4583
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.22 (0.28), residues: 1067
  helix:  1.12 (0.25), residues: 507
  sheet: -1.52 (0.30), residues: 268
  loop :  0.45 (0.42), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 100 
 TYR   0.007   0.001   TYR C  36 
 PHE   0.007   0.001   PHE E 132 
 TRP   0.001   0.000   TRP D 135 
 HIS   0.002   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11086)
  covalent geometry    : angle       0.53399 (15439)
  hydrogen bonds       : bond        0.13290 (  428)
  hydrogen bonds       : angle       5.89058 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: B   70 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8079 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1478
  time to fit residues: 42.6481
Evaluate side-chains
  174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
C 103 GLN
** G  58 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.181358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.125365 restraints weight = 11355.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.24
r_work: 0.3272 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11086  Z= 0.159
  Angle     :  0.561   7.081  15439  Z= 0.306
  Chirality :  0.039   0.146   1803
  Planarity :  0.004   0.032   1598
  Dihedral  : 23.708 151.894   2423
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  6.87 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.22 (0.28), residues: 1067
  helix:  0.98 (0.24), residues: 511
  sheet: -1.35 (0.29), residues: 278
  loop :  0.65 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  77 
 TYR   0.007   0.001   TYR F  36 
 PHE   0.010   0.002   PHE F  63 
 TRP   0.002   0.000   TRP D 135 
 HIS   0.006   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11086)
  covalent geometry    : angle       0.56100 (15439)
  hydrogen bonds       : bond        0.04483 (  428)
  hydrogen bonds       : angle       4.62660 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 181
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8166 (mt-10)
REVERT: C  112 LYS cc_start: 0.8041 (mptt) cc_final: 0.7840 (mmtm)
REVERT: C  122 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7102 (mp0)
REVERT: E  100 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6906 (ttp80)
REVERT: F  101 CYS cc_start: 0.6741 (m) cc_final: 0.6493 (m)
REVERT: G   77 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7887 (ttp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 186
  average time/residue: 0.1540
  time to fit residues: 36.2497
Evaluate side-chains
  174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 168
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain F residue  102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0980
   chunk 84 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0040
   chunk 61 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0030
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.3002

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4125 r_free = 0.4125 target = 0.179544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.124867 restraints weight = 11466.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.25
r_work: 0.3209 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11086  Z= 0.113
  Angle     :  0.505   5.845  15439  Z= 0.281
  Chirality :  0.037   0.133   1803
  Planarity :  0.004   0.032   1598
  Dihedral  : 23.728 152.643   2423
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.73 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.34 (0.28), residues: 1067
  helix:  1.09 (0.24), residues: 512
  sheet: -1.34 (0.29), residues: 280
  loop :  0.75 (0.44), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  67 
 TYR   0.009   0.000   TYR F  36 
 PHE   0.008   0.001   PHE F  63 
 TRP   0.001   0.000   TRP E 135 
 HIS   0.004   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11086)
  covalent geometry    : angle       0.50499 (15439)
  hydrogen bonds       : bond        0.03831 (  428)
  hydrogen bonds       : angle       4.18825 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 186
  time to evaluate  : 0.388 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8211 (mt-10)
REVERT: C   77 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7697 (ttm-80)
REVERT: C  112 LYS cc_start: 0.8046 (mptt) cc_final: 0.7732 (mmtm)
REVERT: C  122 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7139 (mp0)
REVERT: D  106 ASP cc_start: 0.7768 (t0) cc_final: 0.7461 (t0)
REVERT: D  129 LYS cc_start: 0.7918 (tppt) cc_final: 0.7699 (tppt)
REVERT: E   32 MET cc_start: 0.7754 (mmm) cc_final: 0.7356 (mmm)
REVERT: E   65 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8096 (mm-30)
REVERT: E  100 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6938 (ttp80)
REVERT: F  101 CYS cc_start: 0.6764 (m) cc_final: 0.6511 (m)
REVERT: F  122 GLU cc_start: 0.7195 (tp30) cc_final: 0.6902 (tp30)
REVERT: G   93 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7598 (pp)
  outliers start: 11
  outliers final: 4
  residues processed: 191
  average time/residue: 0.1546
  time to fit residues: 37.5702
Evaluate side-chains
  177 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0070
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4139 r_free = 0.4139 target = 0.181197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121691 restraints weight = 11661.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.18
r_work: 0.3232 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11086  Z= 0.124
  Angle     :  0.512   6.057  15439  Z= 0.282
  Chirality :  0.037   0.135   1803
  Planarity :  0.003   0.031   1598
  Dihedral  : 23.739 152.566   2423
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.92 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.34 (0.27), residues: 1067
  helix:  1.08 (0.24), residues: 513
  sheet: -1.33 (0.29), residues: 280
  loop :  0.76 (0.44), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  77 
 TYR   0.006   0.000   TYR F  36 
 PHE   0.009   0.002   PHE F  63 
 TRP   0.002   0.000   TRP E 135 
 HIS   0.005   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11086)
  covalent geometry    : angle       0.51203 (15439)
  hydrogen bonds       : bond        0.03826 (  428)
  hydrogen bonds       : angle       4.08360 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8398 (mt-10)
REVERT: C   17 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8126 (mt)
REVERT: C   77 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7599 (ttm-80)
REVERT: C  112 LYS cc_start: 0.8120 (mptt) cc_final: 0.7735 (mptt)
REVERT: C  122 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7116 (mp0)
REVERT: D  106 ASP cc_start: 0.7741 (t0) cc_final: 0.7260 (t0)
REVERT: E   32 MET cc_start: 0.7909 (mmm) cc_final: 0.7474 (mmm)
REVERT: E  100 ARG cc_start: 0.7219 (ttp80) cc_final: 0.6966 (tmm160)
REVERT: E  118 LYS cc_start: 0.7945 (mptt) cc_final: 0.7652 (mtpp)
REVERT: F  101 CYS cc_start: 0.6699 (m) cc_final: 0.6463 (m)
REVERT: G   93 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7505 (pp)
  outliers start: 15
  outliers final: 8
  residues processed: 182
  average time/residue: 0.1670
  time to fit residues: 38.0757
Evaluate side-chains
  183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 26 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
C  79 ASN
** G  58 HIS ** 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 = 0.4134 r_free = 0.4134 target = 0.181381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117025 restraints weight = 11544.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.17
r_work: 0.3204 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11086  Z= 0.136
  Angle     :  0.515   5.962  15439  Z= 0.282
  Chirality :  0.037   0.133   1803
  Planarity :  0.003   0.031   1598
  Dihedral  : 23.749 152.791   2423
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.56 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.47 (0.27), residues: 1067
  helix:  1.22 (0.24), residues: 499
  sheet: -1.34 (0.28), residues: 280
  loop :  0.88 (0.43), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  67 
 TYR   0.007   0.001   TYR F  36 
 PHE   0.008   0.002   PHE B  63 
 TRP   0.003   0.000   TRP D 135 
 HIS   0.005   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11086)
  covalent geometry    : angle       0.51522 (15439)
  hydrogen bonds       : bond        0.03852 (  428)
  hydrogen bonds       : angle       4.06554 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.395 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8374 (mt-10)
REVERT: C   17 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8162 (mt)
REVERT: C   32 MET cc_start: 0.8000 (mmt) cc_final: 0.7710 (mmt)
REVERT: C   77 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7641 (ttm-80)
REVERT: C  112 LYS cc_start: 0.8118 (mptt) cc_final: 0.7703 (mptt)
REVERT: C  122 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7138 (mp0)
REVERT: D  106 ASP cc_start: 0.7808 (t0) cc_final: 0.7304 (t0)
REVERT: E   32 MET cc_start: 0.7932 (mmm) cc_final: 0.7504 (mmm)
REVERT: E  100 ARG cc_start: 0.7247 (ttp80) cc_final: 0.6953 (tmm160)
REVERT: F  101 CYS cc_start: 0.6631 (m) cc_final: 0.6382 (m)
REVERT: F  122 GLU cc_start: 0.7197 (tp30) cc_final: 0.6956 (tp30)
REVERT: G   93 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7536 (pp)
  outliers start: 17
  outliers final: 8
  residues processed: 187
  average time/residue: 0.1548
  time to fit residues: 36.8252
Evaluate side-chains
  187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  112 LYS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4125 r_free = 0.4125 target = 0.180518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.115003 restraints weight = 11612.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.13
r_work: 0.3178 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11086  Z= 0.165
  Angle     :  0.543   6.281  15439  Z= 0.292
  Chirality :  0.038   0.130   1803
  Planarity :  0.004   0.030   1598
  Dihedral  : 23.795 153.144   2423
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.88 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.38 (0.27), residues: 1067
  helix:  1.15 (0.24), residues: 497
  sheet: -1.40 (0.28), residues: 280
  loop :  0.83 (0.42), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  67 
 TYR   0.005   0.001   TYR F  36 
 PHE   0.010   0.002   PHE D 132 
 TRP   0.005   0.001   TRP D 135 
 HIS   0.006   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (11086)
  covalent geometry    : angle       0.54344 (15439)
  hydrogen bonds       : bond        0.04082 (  428)
  hydrogen bonds       : angle       4.14312 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.358 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8375 (mt-10)
REVERT: C   17 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8187 (mt)
REVERT: C   32 MET cc_start: 0.8033 (mmt) cc_final: 0.7756 (mmt)
REVERT: C   77 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7659 (ttm-80)
REVERT: C  101 CYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6675 (m)
REVERT: C  112 LYS cc_start: 0.8122 (mptt) cc_final: 0.7824 (tptp)
REVERT: D  106 ASP cc_start: 0.7819 (t0) cc_final: 0.7375 (t0)
REVERT: E   32 MET cc_start: 0.7952 (mmm) cc_final: 0.7515 (mmm)
REVERT: E  100 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6981 (tmm160)
REVERT: E  118 LYS cc_start: 0.8026 (mptt) cc_final: 0.7720 (mtpp)
REVERT: F   97 GLU cc_start: 0.7579 (mp0) cc_final: 0.6989 (mp0)
REVERT: F  101 CYS cc_start: 0.6632 (m) cc_final: 0.6414 (m)
REVERT: G   93 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7541 (pp)
  outliers start: 20
  outliers final: 11
  residues processed: 190
  average time/residue: 0.1515
  time to fit residues: 36.4924
Evaluate side-chains
  186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  112 LYS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  101 CYS
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0570
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.179945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.115733 restraints weight = 11484.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.06
r_work: 0.3213 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11086  Z= 0.157
  Angle     :  0.541   6.166  15439  Z= 0.293
  Chirality :  0.038   0.132   1803
  Planarity :  0.004   0.030   1598
  Dihedral  : 23.791 153.225   2423
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.31 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.35 (0.27), residues: 1067
  helix:  1.10 (0.24), residues: 497
  sheet: -1.40 (0.28), residues: 280
  loop :  0.84 (0.43), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  67 
 TYR   0.006   0.001   TYR F  36 
 PHE   0.008   0.002   PHE D 132 
 TRP   0.004   0.001   TRP D 135 
 HIS   0.005   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (11086)
  covalent geometry    : angle       0.54103 (15439)
  hydrogen bonds       : bond        0.04022 (  428)
  hydrogen bonds       : angle       4.15608 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.374 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8394 (mt-10)
REVERT: C   17 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8194 (mt)
REVERT: C   32 MET cc_start: 0.8056 (mmt) cc_final: 0.7810 (mmt)
REVERT: C   77 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7627 (ttm-80)
REVERT: C  101 CYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6716 (m)
REVERT: C  112 LYS cc_start: 0.8153 (mptt) cc_final: 0.7867 (tptp)
REVERT: D  106 ASP cc_start: 0.7844 (t0) cc_final: 0.7420 (t0)
REVERT: E   32 MET cc_start: 0.7943 (mmm) cc_final: 0.7505 (mmm)
REVERT: E  100 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6998 (tmm160)
REVERT: E  123 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7363 (mtp85)
REVERT: E  127 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6844 (mt-10)
REVERT: F  101 CYS cc_start: 0.6690 (m) cc_final: 0.6487 (m)
REVERT: G   93 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7585 (pp)
  outliers start: 17
  outliers final: 9
  residues processed: 184
  average time/residue: 0.1627
  time to fit residues: 37.8757
Evaluate side-chains
  190 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  112 LYS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  101 CYS
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 92 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4149 r_free = 0.4149 target = 0.181348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123055 restraints weight = 11529.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.25
r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11086  Z= 0.141
  Angle     :  0.534   6.079  15439  Z= 0.290
  Chirality :  0.038   0.132   1803
  Planarity :  0.004   0.030   1598
  Dihedral  : 23.758 153.176   2423
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.63 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.37 (0.27), residues: 1067
  helix:  1.12 (0.24), residues: 497
  sheet: -1.40 (0.28), residues: 280
  loop :  0.88 (0.43), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  67 
 TYR   0.006   0.001   TYR F  36 
 PHE   0.008   0.002   PHE D 132 
 TRP   0.004   0.000   TRP D 135 
 HIS   0.005   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11086)
  covalent geometry    : angle       0.53445 (15439)
  hydrogen bonds       : bond        0.03918 (  428)
  hydrogen bonds       : angle       4.13785 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8214 (mt-10)
REVERT: C   17 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8107 (mt)
REVERT: C   32 MET cc_start: 0.8016 (mmt) cc_final: 0.7748 (mmt)
REVERT: C   77 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7430 (ttm-80)
REVERT: C  101 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6729 (m)
REVERT: C  112 LYS cc_start: 0.8102 (mptt) cc_final: 0.7853 (tptp)
REVERT: D  106 ASP cc_start: 0.7827 (t0) cc_final: 0.7446 (t0)
REVERT: D  129 LYS cc_start: 0.7892 (tppt) cc_final: 0.7573 (tptt)
REVERT: E   32 MET cc_start: 0.7813 (mmm) cc_final: 0.7374 (mmm)
REVERT: E  100 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7107 (tmm160)
REVERT: E  118 LYS cc_start: 0.8052 (mptt) cc_final: 0.7783 (mtpp)
REVERT: E  123 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7381 (mtp85)
REVERT: E  127 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6868 (mt-10)
REVERT: F  101 CYS cc_start: 0.6852 (m) cc_final: 0.6608 (m)
REVERT: G   93 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7610 (pp)
REVERT: H  123 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7347 (mmm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 178
  average time/residue: 0.1629
  time to fit residues: 36.2901
Evaluate side-chains
  185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  101 CYS
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4147 r_free = 0.4147 target = 0.181068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.117394 restraints weight = 11556.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.04
r_work: 0.3222 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11086  Z= 0.147
  Angle     :  0.539   6.163  15439  Z= 0.292
  Chirality :  0.038   0.132   1803
  Planarity :  0.004   0.049   1598
  Dihedral  : 23.759 153.214   2423
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.63 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.37 (0.27), residues: 1067
  helix:  1.12 (0.24), residues: 496
  sheet: -1.39 (0.28), residues: 280
  loop :  0.86 (0.42), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  67 
 TYR   0.006   0.001   TYR F  36 
 PHE   0.008   0.002   PHE B  63 
 TRP   0.004   0.001   TRP D 135 
 HIS   0.005   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11086)
  covalent geometry    : angle       0.53937 (15439)
  hydrogen bonds       : bond        0.03957 (  428)
  hydrogen bonds       : angle       4.14889 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 0.372 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8345 (mt-10)
REVERT: C   17 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8170 (mt)
REVERT: C   32 MET cc_start: 0.8062 (mmt) cc_final: 0.7793 (mmt)
REVERT: C   77 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7584 (ttm-80)
REVERT: C  101 CYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6719 (m)
REVERT: C  112 LYS cc_start: 0.8164 (mptt) cc_final: 0.7878 (tptp)
REVERT: D  106 ASP cc_start: 0.7873 (t0) cc_final: 0.7459 (t0)
REVERT: E   32 MET cc_start: 0.7936 (mmm) cc_final: 0.7479 (mmm)
REVERT: E  100 ARG cc_start: 0.7370 (ttp80) cc_final: 0.7084 (tmm160)
REVERT: E  118 LYS cc_start: 0.8032 (mptt) cc_final: 0.7730 (mtpp)
REVERT: E  123 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7341 (mtp85)
REVERT: E  127 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6857 (mt-10)
REVERT: F  101 CYS cc_start: 0.6815 (m) cc_final: 0.6585 (m)
REVERT: G   93 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7593 (pp)
REVERT: H  123 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7370 (mmm-85)
  outliers start: 15
  outliers final: 9
  residues processed: 181
  average time/residue: 0.1617
  time to fit residues: 37.0010
Evaluate side-chains
  184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  101 CYS
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0270
   chunk 108 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4149 r_free = 0.4149 target = 0.181373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.123320 restraints weight = 11426.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.24
r_work: 0.3170 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11086  Z= 0.138
  Angle     :  0.534   5.958  15439  Z= 0.290
  Chirality :  0.037   0.132   1803
  Planarity :  0.004   0.030   1598
  Dihedral  : 23.732 153.152   2423
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.96 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.37 (0.27), residues: 1067
  helix:  1.11 (0.24), residues: 497
  sheet: -1.39 (0.28), residues: 280
  loop :  0.89 (0.43), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  67 
 TYR   0.006   0.001   TYR F  36 
 PHE   0.008   0.002   PHE F  63 
 TRP   0.003   0.000   TRP D 135 
 HIS   0.004   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11086)
  covalent geometry    : angle       0.53398 (15439)
  hydrogen bonds       : bond        0.03877 (  428)
  hydrogen bonds       : angle       4.15289 ( 1191)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.397 
Fit side-chains
REVERT: B   68 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8203 (mt-10)
REVERT: C   17 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8103 (mt)
REVERT: C   32 MET cc_start: 0.8011 (mmt) cc_final: 0.7718 (mmt)
REVERT: C  101 CYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6743 (m)
REVERT: C  112 LYS cc_start: 0.8111 (mptt) cc_final: 0.7864 (tptp)
REVERT: D  106 ASP cc_start: 0.7860 (t0) cc_final: 0.7483 (t0)
REVERT: E   32 MET cc_start: 0.7811 (mmm) cc_final: 0.7371 (mmm)
REVERT: E  100 ARG cc_start: 0.7366 (ttp80) cc_final: 0.7089 (tmm160)
REVERT: E  118 LYS cc_start: 0.8081 (mptt) cc_final: 0.7816 (mtpp)
REVERT: E  123 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7378 (mtp85)
REVERT: E  127 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6861 (mt-10)
REVERT: F  101 CYS cc_start: 0.6866 (m) cc_final: 0.6624 (m)
REVERT: G   93 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7599 (pp)
REVERT: H  123 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7369 (mmm-85)
  outliers start: 13
  outliers final: 9
  residues processed: 176
  average time/residue: 0.1644
  time to fit residues: 36.6412
Evaluate side-chains
  185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 PHE
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   28 VAL
Chi-restraints excluded: chain C residue   97 GLU
Chi-restraints excluded: chain C residue  101 CYS
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  109 THR
Chi-restraints excluded: chain G residue   93 LEU
Chi-restraints excluded: chain H residue  122 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
C  22 ASN
** G  58 HIS ** 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 = 0.4154 r_free = 0.4154 target = 0.182249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124863 restraints weight = 11577.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.43
r_work: 0.3132 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11086  Z= 0.175
  Angle     :  0.565   6.518  15439  Z= 0.301
  Chirality :  0.039   0.132   1803
  Planarity :  0.004   0.034   1598
  Dihedral  : 23.779 153.435   2423
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.17 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.29 (0.27), residues: 1067
  helix:  1.03 (0.24), residues: 497
  sheet: -1.40 (0.28), residues: 280
  loop :  0.81 (0.42), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  67 
 TYR   0.007   0.001   TYR F  36 
 PHE   0.010   0.002   PHE D 132 
 TRP   0.005   0.001   TRP D 135 
 HIS   0.006   0.001   HIS H  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (11086)
  covalent geometry    : angle       0.56455 (15439)
  hydrogen bonds       : bond        0.04198 (  428)
  hydrogen bonds       : angle       4.20628 ( 1191)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3299.74 seconds
wall clock time: 56 minutes 51.52 seconds (3411.52 seconds total)