Starting phenix.real_space_refine
on Fri Sep 11 21:33:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6se0_10151/09_2026/6se0_10151.map"
  }
  resolution = 3.8
  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=   0.003
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     288      5.49       5
     S      10      5.16       5
     C    6657      2.51       5
     N    2256      2.21       5
     O    2791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12002
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 845
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.77, per 1000 atoms: 0.23
  Number of scatterers: 12002
  At special positions: 0
  Unit cell: (75.26, 119.78, 115.54, 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      10     16.00
     P     288     15.00
     O    2791      8.00
     N    2256      7.00
     C    6657      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 380.2 milliseconds
  

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1414

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      70.8% alpha, 2.6% beta
      145 base pairs and 257 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 57
      removed outlier: 3.806A  pdb=" N   GLU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.824A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.509A  pdb=" N   ALA A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 134 through 139
      removed outlier: 3.783A  pdb=" N   LEU A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.593A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.202A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.583A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.616A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 98
      removed outlier: 3.700A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.664A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.547A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.520A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 122
      removed outlier: 3.522A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.838A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.602A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA E 116 " --> pdb=" O   LEU E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.804A  pdb=" N   GLY E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.542A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.289A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.509A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 38
      removed outlier: 3.799A  pdb=" N   ASN G  38 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.550A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.582A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.577A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 122
      removed outlier: 3.591A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 7.240A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.870A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.015A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.527A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    377 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      257 stacking parallelities
  Total time for adding SS restraints: 2.19

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2004
        1.33 -     1.45: 4338
        1.45 -     1.57: 5874
        1.57 -     1.68: 576
        1.68 -     1.80: 18
  Bond restraints: 12810
  Sorted by residual:
  bond pdb=" C3'  DA J   6 "
       pdb=" O3'  DA J   6 "
    ideal  model  delta    sigma   weight residual
    1.435  1.358  0.077 1.30e-02 5.92e+03 3.51e+01
  bond pdb=" C3'  DC J -11 "
       pdb=" O3'  DC J -11 "
    ideal  model  delta    sigma   weight residual
    1.435  1.375  0.060 1.30e-02 5.92e+03 2.16e+01
  bond pdb=" C3'  DA J -14 "
       pdb=" O3'  DA J -14 "
    ideal  model  delta    sigma   weight residual
    1.435  1.379  0.056 1.30e-02 5.92e+03 1.83e+01
  bond pdb=" C3'  DA J -55 "
       pdb=" O3'  DA J -55 "
    ideal  model  delta    sigma   weight residual
    1.435  1.382  0.053 1.30e-02 5.92e+03 1.65e+01
  bond pdb=" C3'  DG J -35 "
       pdb=" O3'  DG J -35 "
    ideal  model  delta    sigma   weight residual
    1.435  1.382  0.053 1.30e-02 5.92e+03 1.64e+01
  ... (remaining 12805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.52: 18341
        3.52 -     7.04: 175
        7.04 -    10.57: 17
       10.57 -    14.09: 1
       14.09 -    17.61: 1
  Bond angle restraints: 18535
  Sorted by residual:
  angle pdb=" O5'  DC J -58 "
        pdb=" C5'  DC J -58 "
        pdb=" C4'  DC J -58 "
      ideal   model   delta    sigma   weight residual
     109.40  114.10   -4.70 8.00e-01 1.56e+00 3.45e+01
  angle pdb=" O5'  DG J  57 "
        pdb=" C5'  DG J  57 "
        pdb=" C4'  DG J  57 "
      ideal   model   delta    sigma   weight residual
     109.40  113.55   -4.15 8.00e-01 1.56e+00 2.69e+01
  angle pdb=" O5'  DG J  -5 "
        pdb=" C5'  DG J  -5 "
        pdb=" C4'  DG J  -5 "
      ideal   model   delta    sigma   weight residual
     109.40  113.49   -4.09 8.00e-01 1.56e+00 2.61e+01
  angle pdb=" CA  LEU F  90 "
        pdb=" CB  LEU F  90 "
        pdb=" CG  LEU F  90 "
      ideal   model   delta    sigma   weight residual
     116.30   98.69   17.61 3.50e+00 8.16e-02 2.53e+01
  angle pdb=" O4'  DA J -72 "
        pdb=" C1'  DA J -72 "
        pdb=" N9   DA J -72 "
      ideal   model   delta    sigma   weight residual
     108.00  111.42   -3.42 7.00e-01 2.04e+00 2.39e+01
  ... (remaining 18530 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.26: 5109
       29.26 -    58.52: 1726
       58.52 -    87.78: 87
       87.78 -   117.04: 3
      117.04 -   146.30: 1
  Dihedral angle restraints: 6926
    sinusoidal: 4729
      harmonic: 2197
  Sorted by residual:
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.46  -19.54     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.70  146.30     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" CA  GLN G 112 "
           pdb=" C   GLN G 112 "
           pdb=" N   ALA G 113 "
           pdb=" CA  ALA G 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.04  -16.96     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 6923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1378
       0.058 -    0.116: 596
       0.116 -    0.175: 109
       0.175 -    0.233: 12
       0.233 -    0.291: 4
  Chirality restraints: 2099
  Sorted by residual:
  chirality pdb=" CG  LEU G 108 "
            pdb=" CB  LEU G 108 "
            pdb=" CD1 LEU G 108 "
            pdb=" CD2 LEU G 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" P    DG J  50 "
            pdb=" OP1  DG J  50 "
            pdb=" OP2  DG J  50 "
            pdb=" O5'  DG J  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.60   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 2096 not shown)

  Planarity restraints: 1338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.063 5.00e-02 4.00e+02   9.47e-02 1.44e+01
        pdb=" N   PRO G  80 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.058 5.00e-02 4.00e+02   8.80e-02 1.24e+01
        pdb=" N   PRO C  80 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 119 "    0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   VAL A 119 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   VAL A 119 "    0.020 2.00e-02 2.50e+03
        pdb=" N   THR A 120 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1335 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2322
        2.78 -     3.31: 10081
        3.31 -     3.84: 23976
        3.84 -     4.37: 26839
        4.37 -     4.90: 37586
  Nonbonded interactions: 100804
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   LEU G  23 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O2   DC I -56 "
            pdb=" N2   DG J  56 "
     model   vdw
     2.286 2.496
  nonbonded pdb=" O2   DC I -62 "
            pdb=" N2   DG J  62 "
     model   vdw
     2.299 2.496
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" O   THR E 120 "
     model   vdw
     2.343 3.040
  ... (remaining 100799 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 10 through 116)
  selection = (chain 'G' and resid 10 through 116)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:         0.050
  Set scattering table:                    0.030
  Process input model:                     13.210
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
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      :  0.009   0.077  12810  Z= 0.769
  Angle     :  1.124  17.610  18535  Z= 0.860
  Chirality :  0.063   0.291   2099
  Planarity :  0.008   0.095   1338
  Dihedral  : 28.079 146.298   5512
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.23), residues: 749
  helix: -1.67 (0.17), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.94 (0.31), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  44 
 TYR   0.035   0.004   TYR A 110 
 PHE   0.025   0.004   PHE A  78 
 TRP   0.018   0.002   TRP E  86 
 HIS   0.015   0.003   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00944 /  0.77 (12810)
  covalent geometry    : angle       1.12430 /  0.86 (18535)
  hydrogen bonds       : bond        0.12059 /  7.97 (  745)
  hydrogen bonds       : angle       4.17951 /  2.99 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9426 (tp30) cc_final: 0.9174 (tp30)
REVERT: A   85 ASN cc_start: 0.8494 (m-40) cc_final: 0.8175 (m-40)
REVERT: B   45 ARG cc_start: 0.7613 (mtm180) cc_final: 0.6524 (ttm110)
REVERT: C   56 GLU cc_start: 0.6795 (tt0) cc_final: 0.6576 (tt0)
REVERT: C   57 TYR cc_start: 0.9003 (t80) cc_final: 0.8528 (t80)
REVERT: C   61 GLU cc_start: 0.8731 (tp30) cc_final: 0.8262 (tp30)
REVERT: C   92 GLU cc_start: 0.8295 (tt0) cc_final: 0.7903 (tt0)
REVERT: C   95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7929 (tppt)
REVERT: D   86 ARG cc_start: 0.8355 (mmt180) cc_final: 0.7895 (mtp85)
REVERT: D  113 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7847 (mt-10)
REVERT: D  116 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8555 (ttmm)
REVERT: E   49 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8453 (ptmt)
REVERT: E   64 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7371 (tptt)
REVERT: E   73 GLU cc_start: 0.9093 (tp30) cc_final: 0.8453 (tp30)
REVERT: F   79 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7352 (mtpp)
REVERT: G   39 TYR cc_start: 0.8417 (m-80) cc_final: 0.8217 (m-80)
REVERT: G   71 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.7952 (mtm-85)
REVERT: G   92 GLU cc_start: 0.8177 (tt0) cc_final: 0.7792 (tt0)
REVERT: H   93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8066 (mm-30)
REVERT: H   95 GLN cc_start: 0.8108 (tt0) cc_final: 0.7145 (tm-30)
REVERT: H  105 GLU cc_start: 0.8171 (tp30) cc_final: 0.7551 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1560
  time to fit residues: 52.5027
Evaluate side-chains
  186 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
A 104 HIS
B  64 ASN
D  95 GLN
G  31 HIS
G  73 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.128849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.091783 restraints weight = 32495.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.095320 restraints weight = 16258.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.097660 restraints weight = 10439.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099213 restraints weight = 7906.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.100109 restraints weight = 6685.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12810  Z= 0.158
  Angle     :  0.735  10.973  18535  Z= 0.413
  Chirality :  0.049   0.223   2099
  Planarity :  0.005   0.069   1338
  Dihedral  : 30.804 150.890   4015
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 18.18 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.27), residues: 749
  helix:  0.29 (0.21), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.58 (0.34), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  52 
 TYR   0.013   0.002   TYR G  50 
 PHE   0.009   0.001   PHE E 122 
 TRP   0.018   0.003   TRP E  47 
 HIS   0.005   0.001   HIS E 115 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.16 (12810)
  covalent geometry    : angle       0.73546 /  0.41 (18535)
  hydrogen bonds       : bond        0.06260 /  4.11 (  745)
  hydrogen bonds       : angle       3.42123 /  2.42 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9404 (tp30) cc_final: 0.9179 (tp30)
REVERT: A   85 ASN cc_start: 0.8405 (m-40) cc_final: 0.8110 (m-40)
REVERT: B   44 LYS cc_start: 0.8419 (tttt) cc_final: 0.8118 (mmmt)
REVERT: B   84 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7294 (mtm)
REVERT: C   25 PHE cc_start: 0.7622 (m-80) cc_final: 0.7308 (m-80)
REVERT: C   56 GLU cc_start: 0.6570 (tt0) cc_final: 0.6072 (tt0)
REVERT: C   57 TYR cc_start: 0.9018 (t80) cc_final: 0.8347 (t80)
REVERT: C   61 GLU cc_start: 0.8692 (tp30) cc_final: 0.8240 (tp30)
REVERT: D  113 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: E   49 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8459 (ptmt)
REVERT: E   62 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7289 (tt)
REVERT: E   64 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7226 (tptt)
REVERT: E   73 GLU cc_start: 0.9013 (tp30) cc_final: 0.8353 (tm-30)
REVERT: E  107 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8621 (tp30)
REVERT: E  127 GLN cc_start: 0.8440 (tt0) cc_final: 0.7730 (pt0)
REVERT: F   31 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7526 (tttt)
REVERT: F   50 ILE cc_start: 0.8292 (tp) cc_final: 0.7783 (mm)
REVERT: G   64 GLU cc_start: 0.8818 (tp30) cc_final: 0.8473 (mm-30)
REVERT: G   71 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.7893 (ptp-170)
REVERT: G   92 GLU cc_start: 0.7931 (tt0) cc_final: 0.7631 (tt0)
REVERT: H   93 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: H   95 GLN cc_start: 0.7851 (tt0) cc_final: 0.7137 (tm-30)
REVERT: H  105 GLU cc_start: 0.7989 (tp30) cc_final: 0.7583 (tp30)
  outliers start: 27
  outliers final: 15
  residues processed: 219
  average time/residue: 0.1190
  time to fit residues: 36.4174
Evaluate side-chains
  201 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue  107 GLU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 85 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0020
   chunk 91 optimal weight:   30.0000
   chunk 45 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.2590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  31 HIS
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** 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 = 0.4182 r_free = 0.4182 target = 0.128201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.091228 restraints weight = 32856.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.094749 restraints weight = 16544.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.097143 restraints weight = 10630.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.098701 restraints weight = 8053.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099601 restraints weight = 6814.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12810  Z= 0.149
  Angle     :  0.678  10.552  18535  Z= 0.387
  Chirality :  0.045   0.195   2099
  Planarity :  0.005   0.056   1338
  Dihedral  : 30.732 150.384   4015
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 20.41 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.29), residues: 749
  helix:  0.81 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.36 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  29 
 TYR   0.022   0.002   TYR G  57 
 PHE   0.014   0.001   PHE B 100 
 TRP   0.021   0.003   TRP E  47 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.15 (12810)
  covalent geometry    : angle       0.67768 /  0.39 (18535)
  hydrogen bonds       : bond        0.05525 /  3.63 (  745)
  hydrogen bonds       : angle       3.23931 /  2.31 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9383 (tp30) cc_final: 0.9167 (tp30)
REVERT: A   85 ASN cc_start: 0.8578 (m-40) cc_final: 0.8298 (m-40)
REVERT: A  110 TYR cc_start: 0.7737 (t80) cc_final: 0.7403 (t80)
REVERT: B   44 LYS cc_start: 0.8561 (tttt) cc_final: 0.7921 (mmmt)
REVERT: B   45 ARG cc_start: 0.7355 (mtm180) cc_final: 0.6613 (mtt90)
REVERT: B   84 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7278 (mtm)
REVERT: C   56 GLU cc_start: 0.6602 (tt0) cc_final: 0.6248 (tt0)
REVERT: C   57 TYR cc_start: 0.8989 (t80) cc_final: 0.8216 (t80)
REVERT: C   64 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7853 (mm-30)
REVERT: C   82 HIS cc_start: 0.7964 (m170) cc_final: 0.7696 (m90)
REVERT: C   92 GLU cc_start: 0.7648 (tt0) cc_final: 0.6706 (tt0)
REVERT: D   79 ARG cc_start: 0.7866 (ptp90) cc_final: 0.6897 (ptp90)
REVERT: D  106 LEU cc_start: 0.9468 (tp) cc_final: 0.9050 (mt)
REVERT: D  113 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7623 (mt-10)
REVERT: D  120 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8186 (tttm)
REVERT: E   49 LYS cc_start: 0.8998 (ptmt) cc_final: 0.8390 (ptmt)
REVERT: E   73 GLU cc_start: 0.9035 (tp30) cc_final: 0.8354 (tm-30)
REVERT: F   50 ILE cc_start: 0.8308 (tp) cc_final: 0.7753 (mm)
REVERT: F   79 LYS cc_start: 0.7449 (mtpp) cc_final: 0.6981 (mtpt)
REVERT: G   71 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8012 (mtm180)
REVERT: G   92 GLU cc_start: 0.8075 (tt0) cc_final: 0.7790 (tt0)
REVERT: H   93 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: H   95 GLN cc_start: 0.7952 (tt0) cc_final: 0.7090 (tm-30)
REVERT: H  105 GLU cc_start: 0.7989 (tp30) cc_final: 0.7540 (tp30)
  outliers start: 33
  outliers final: 20
  residues processed: 217
  average time/residue: 0.1101
  time to fit residues: 34.1845
Evaluate side-chains
  204 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 183
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue  106 PHE
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   94 ILE
Chi-restraints excluded: chain H residue  115 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:   30.0000
   chunk 87 optimal weight:   50.0000
   chunk 20 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 78 optimal weight:   30.0000
   chunk 47 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 93 optimal weight:   20.0000
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
E  85 ASN
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.126032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089101 restraints weight = 33335.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.092468 restraints weight = 16960.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.094671 restraints weight = 10991.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.096161 restraints weight = 8408.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.097073 restraints weight = 7149.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12810  Z= 0.194
  Angle     :  0.707  11.389  18535  Z= 0.396
  Chirality :  0.045   0.214   2099
  Planarity :  0.005   0.052   1338
  Dihedral  : 30.793 151.135   4015
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 23.92 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.29), residues: 749
  helix:  0.94 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.43 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  67 
 TYR   0.032   0.003   TYR D  40 
 PHE   0.012   0.002   PHE A  84 
 TRP   0.020   0.002   TRP E  47 
 HIS   0.007   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.19 (12810)
  covalent geometry    : angle       0.70699 /  0.40 (18535)
  hydrogen bonds       : bond        0.05598 /  3.69 (  745)
  hydrogen bonds       : angle       3.34193 /  2.39 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8134 (ttpp)
REVERT: A   85 ASN cc_start: 0.8448 (m-40) cc_final: 0.8129 (m-40)
REVERT: A  110 TYR cc_start: 0.7726 (t80) cc_final: 0.7318 (t80)
REVERT: B   36 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7347 (mtm110)
REVERT: B   44 LYS cc_start: 0.8594 (tttt) cc_final: 0.7929 (mmmt)
REVERT: B   45 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6682 (mtt90)
REVERT: B   84 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7227 (mtm)
REVERT: C   92 GLU cc_start: 0.7823 (tt0) cc_final: 0.6587 (tt0)
REVERT: D  105 GLU cc_start: 0.8918 (pm20) cc_final: 0.8713 (pm20)
REVERT: D  106 LEU cc_start: 0.9461 (tp) cc_final: 0.9059 (mt)
REVERT: D  120 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8268 (tttm)
REVERT: E   49 LYS cc_start: 0.9075 (ptmt) cc_final: 0.8450 (ptmt)
REVERT: E   62 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7133 (tt)
REVERT: E   73 GLU cc_start: 0.9112 (tp30) cc_final: 0.8428 (tm-30)
REVERT: F   31 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7571 (tttt)
REVERT: F   50 ILE cc_start: 0.8320 (tp) cc_final: 0.7792 (mm)
REVERT: G   71 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8051 (mtm180)
REVERT: G   92 GLU cc_start: 0.8146 (tt0) cc_final: 0.7914 (tt0)
REVERT: H   93 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8076 (mm-30)
REVERT: H   95 GLN cc_start: 0.8074 (tt0) cc_final: 0.7061 (tm-30)
  outliers start: 42
  outliers final: 25
  residues processed: 201
  average time/residue: 0.1199
  time to fit residues: 33.6131
Evaluate side-chains
  204 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  120 THR
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 90 optimal weight:   30.0000
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
E  95 GLN
G  68 ASN
** H  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.128530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.091864 restraints weight = 33314.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.095419 restraints weight = 16678.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.097790 restraints weight = 10671.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.099312 restraints weight = 8069.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.100177 restraints weight = 6831.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12810  Z= 0.141
  Angle     :  0.658  10.134  18535  Z= 0.374
  Chirality :  0.043   0.216   2099
  Planarity :  0.004   0.051   1338
  Dihedral  : 30.681 149.179   4015
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 25.36 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.30), residues: 749
  helix:  1.18 (0.23), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.41 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  79 
 TYR   0.037   0.003   TYR H  83 
 PHE   0.009   0.001   PHE E  84 
 TRP   0.022   0.002   TRP E  47 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.14 (12810)
  covalent geometry    : angle       0.65834 /  0.37 (18535)
  hydrogen bonds       : bond        0.05081 /  3.32 (  745)
  hydrogen bonds       : angle       3.06732 /  2.20 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 193
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8173 (ttpp)
REVERT: A   85 ASN cc_start: 0.8430 (m-40) cc_final: 0.8094 (m-40)
REVERT: A  110 TYR cc_start: 0.7688 (t80) cc_final: 0.7429 (t80)
REVERT: B   36 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7189 (mtm110)
REVERT: B   44 LYS cc_start: 0.8638 (tttt) cc_final: 0.8092 (mmmm)
REVERT: B   45 ARG cc_start: 0.7343 (mtm180) cc_final: 0.6527 (tpp80)
REVERT: B   84 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7266 (mtm)
REVERT: B   92 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7333 (tpm170)
REVERT: C   57 TYR cc_start: 0.8736 (t80) cc_final: 0.8068 (t80)
REVERT: C   82 HIS cc_start: 0.7926 (m170) cc_final: 0.7704 (m90)
REVERT: C   92 GLU cc_start: 0.7585 (tt0) cc_final: 0.6768 (tt0)
REVERT: D  106 LEU cc_start: 0.9456 (tp) cc_final: 0.9206 (mt)
REVERT: D  120 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8176 (tttm)
REVERT: E   49 LYS cc_start: 0.9032 (ptmt) cc_final: 0.8391 (ptmt)
REVERT: E   62 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7026 (tt)
REVERT: E   73 GLU cc_start: 0.9068 (tp30) cc_final: 0.8344 (tp30)
REVERT: F   50 ILE cc_start: 0.8182 (tp) cc_final: 0.7729 (mm)
REVERT: F   79 LYS cc_start: 0.7522 (mtpp) cc_final: 0.7112 (mtpt)
REVERT: F   93 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8031 (tt0)
REVERT: G   71 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.7911 (ptp-110)
REVERT: H   95 GLN cc_start: 0.8010 (tt0) cc_final: 0.7001 (tm-30)
  outliers start: 35
  outliers final: 24
  residues processed: 210
  average time/residue: 0.1182
  time to fit residues: 34.9298
Evaluate side-chains
  204 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   42 TYR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 92 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 73 optimal weight:   50.0000
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
** H  49 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 = 0.4208 r_free = 0.4208 target = 0.129066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.093137 restraints weight = 34052.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.096636 restraints weight = 17101.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.098975 restraints weight = 10929.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100473 restraints weight = 8265.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.101419 restraints weight = 6989.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12810  Z= 0.140
  Angle     :  0.661  10.429  18535  Z= 0.373
  Chirality :  0.043   0.206   2099
  Planarity :  0.004   0.052   1338
  Dihedral  : 30.645 149.989   4015
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.27 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.30), residues: 749
  helix:  1.15 (0.23), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.27 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  79 
 TYR   0.038   0.003   TYR H  83 
 PHE   0.008   0.001   PHE G  25 
 TRP   0.023   0.003   TRP E  47 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.14 (12810)
  covalent geometry    : angle       0.66068 /  0.37 (18535)
  hydrogen bonds       : bond        0.04980 /  3.26 (  745)
  hydrogen bonds       : angle       3.07256 /  2.21 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8171 (ttpp)
REVERT: B   44 LYS cc_start: 0.8620 (tttt) cc_final: 0.7972 (mmmt)
REVERT: B   45 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6370 (tpp80)
REVERT: B   84 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7154 (mtm)
REVERT: B   92 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7155 (tpm170)
REVERT: C   82 HIS cc_start: 0.7969 (m170) cc_final: 0.7762 (m90)
REVERT: C   92 GLU cc_start: 0.7577 (tt0) cc_final: 0.6922 (tt0)
REVERT: D  106 LEU cc_start: 0.9440 (tp) cc_final: 0.9216 (mt)
REVERT: E   49 LYS cc_start: 0.9011 (ptmt) cc_final: 0.8361 (ptmt)
REVERT: E   73 GLU cc_start: 0.9062 (tp30) cc_final: 0.8345 (tp30)
REVERT: F   50 ILE cc_start: 0.8064 (tp) cc_final: 0.7571 (mm)
REVERT: F   53 GLU cc_start: 0.8096 (tt0) cc_final: 0.7855 (tt0)
REVERT: F   79 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7021 (mtpt)
REVERT: F   93 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8035 (tt0)
REVERT: G   71 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.7941 (ptp-110)
REVERT: H   93 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: H   95 GLN cc_start: 0.7968 (tt0) cc_final: 0.7177 (tm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 199
  average time/residue: 0.1093
  time to fit residues: 30.9756
Evaluate side-chains
  200 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 85 optimal weight:   30.0000
   chunk 8 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  89 ASN
** H  49 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 = 0.4220 r_free = 0.4220 target = 0.125385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.091582 restraints weight = 32026.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.094782 restraints weight = 16449.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.096940 restraints weight = 10652.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.098308 restraints weight = 8111.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099174 restraints weight = 6903.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12810  Z= 0.173
  Angle     :  0.689  11.719  18535  Z= 0.386
  Chirality :  0.043   0.303   2099
  Planarity :  0.005   0.050   1338
  Dihedral  : 30.689 150.340   4015
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 26.95 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.75 (0.30), residues: 749
  helix:  1.15 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.16 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  36 
 TYR   0.044   0.003   TYR H  83 
 PHE   0.011   0.001   PHE A  84 
 TRP   0.022   0.002   TRP E  47 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.17 (12810)
  covalent geometry    : angle       0.68885 /  0.39 (18535)
  hydrogen bonds       : bond        0.05198 /  3.41 (  745)
  hydrogen bonds       : angle       3.19476 /  2.31 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 180
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8228 (ttpp)
REVERT: A  110 TYR cc_start: 0.7274 (t80) cc_final: 0.6896 (t80)
REVERT: B   44 LYS cc_start: 0.8638 (tttt) cc_final: 0.8098 (mmmt)
REVERT: B   45 ARG cc_start: 0.7379 (mtm180) cc_final: 0.6333 (tpp80)
REVERT: B   51 TYR cc_start: 0.8032 (m-80) cc_final: 0.7575 (m-80)
REVERT: B   84 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7115 (mtm)
REVERT: B   92 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7400 (tpm170)
REVERT: C   82 HIS cc_start: 0.7956 (m170) cc_final: 0.7752 (m90)
REVERT: C   89 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8532 (m-40)
REVERT: E   49 LYS cc_start: 0.9016 (ptmt) cc_final: 0.8381 (ptmt)
REVERT: E   73 GLU cc_start: 0.9095 (tp30) cc_final: 0.8344 (tp30)
REVERT: F   50 ILE cc_start: 0.8205 (tp) cc_final: 0.7737 (mm)
REVERT: F   53 GLU cc_start: 0.8193 (tt0) cc_final: 0.7913 (tt0)
REVERT: G   71 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.7954 (ptp-110)
REVERT: H   93 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7853 (mm-30)
REVERT: H   95 GLN cc_start: 0.8058 (tt0) cc_final: 0.7248 (tm-30)
  outliers start: 38
  outliers final: 30
  residues processed: 198
  average time/residue: 0.1081
  time to fit residues: 30.7108
Evaluate side-chains
  208 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   89 ASN
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0070
   chunk 75 optimal weight:   30.0000
   chunk 43 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    0.3980
   chunk 84 optimal weight:   30.0000
   overall best weight:    0.6400

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.126736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.093138 restraints weight = 31692.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.096505 restraints weight = 16035.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.098770 restraints weight = 10257.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.100238 restraints weight = 7732.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.101072 restraints weight = 6526.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12810  Z= 0.142
  Angle     :  0.667  11.631  18535  Z= 0.375
  Chirality :  0.042   0.216   2099
  Planarity :  0.004   0.051   1338
  Dihedral  : 30.630 149.376   4015
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 28.71 %
    Favored  : 66.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.30), residues: 749
  helix:  1.20 (0.23), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.19 (0.38), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  86 
 TYR   0.056   0.003   TYR H  83 
 PHE   0.016   0.001   PHE E  84 
 TRP   0.025   0.003   TRP E  47 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.14 (12810)
  covalent geometry    : angle       0.66725 /  0.38 (18535)
  hydrogen bonds       : bond        0.04959 /  3.25 (  745)
  hydrogen bonds       : angle       3.10898 /  2.24 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8235 (ttpp)
REVERT: A  110 TYR cc_start: 0.7172 (t80) cc_final: 0.6886 (t80)
REVERT: B   44 LYS cc_start: 0.8569 (tttt) cc_final: 0.8084 (mmmt)
REVERT: B   45 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6490 (mtt90)
REVERT: B   51 TYR cc_start: 0.7940 (m-80) cc_final: 0.7475 (m-80)
REVERT: B   84 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7084 (mtm)
REVERT: B   92 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7189 (tpm170)
REVERT: C   82 HIS cc_start: 0.7905 (m170) cc_final: 0.7697 (m-70)
REVERT: D   79 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7540 (ptp90)
REVERT: E   49 LYS cc_start: 0.9003 (ptmt) cc_final: 0.8394 (ptmt)
REVERT: E   73 GLU cc_start: 0.9066 (tp30) cc_final: 0.8328 (tp30)
REVERT: F   50 ILE cc_start: 0.8061 (tp) cc_final: 0.7580 (mm)
REVERT: F   93 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8022 (tt0)
REVERT: G   71 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.7931 (ptp-110)
REVERT: H   93 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7842 (mm-30)
REVERT: H   95 GLN cc_start: 0.7992 (tt0) cc_final: 0.7164 (tm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 198
  average time/residue: 0.1139
  time to fit residues: 32.2158
Evaluate side-chains
  204 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:   30.0000
   chunk 49 optimal weight:    3.9990
   chunk 74 optimal weight:   40.0000
   chunk 73 optimal weight:   50.0000
   chunk 79 optimal weight:   30.0000
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 95 optimal weight:   30.0000
   chunk 89 optimal weight:   30.0000
   overall best weight:    3.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.125886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.089862 restraints weight = 34000.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.093109 restraints weight = 17340.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.095256 restraints weight = 11219.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.096638 restraints weight = 8590.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.097491 restraints weight = 7333.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12810  Z= 0.204
  Angle     :  0.728  12.379  18535  Z= 0.404
  Chirality :  0.044   0.229   2099
  Planarity :  0.005   0.049   1338
  Dihedral  : 30.704 150.776   4015
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 28.39 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.30), residues: 749
  helix:  0.99 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.22 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  92 
 TYR   0.065   0.003   TYR H  83 
 PHE   0.016   0.002   PHE A  84 
 TRP   0.022   0.002   TRP E  47 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.20 (12810)
  covalent geometry    : angle       0.72799 /  0.40 (18535)
  hydrogen bonds       : bond        0.05603 /  3.70 (  745)
  hydrogen bonds       : angle       3.41870 /  2.48 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 177
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8202 (ttpp)
REVERT: A  110 TYR cc_start: 0.7299 (t80) cc_final: 0.6982 (t80)
REVERT: B   45 ARG cc_start: 0.7277 (mtm180) cc_final: 0.6922 (tpp80)
REVERT: B   51 TYR cc_start: 0.8133 (m-80) cc_final: 0.7676 (m-80)
REVERT: B   84 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7129 (mtm)
REVERT: C   82 HIS cc_start: 0.7972 (m170) cc_final: 0.7766 (m90)
REVERT: C   89 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8694 (m-40)
REVERT: C   92 GLU cc_start: 0.8369 (mp0) cc_final: 0.8027 (pm20)
REVERT: D   48 VAL cc_start: 0.8274 (p) cc_final: 0.8005 (p)
REVERT: E   49 LYS cc_start: 0.9050 (ptmt) cc_final: 0.8435 (ptmt)
REVERT: E   73 GLU cc_start: 0.9113 (tp30) cc_final: 0.8337 (tp30)
REVERT: F   53 GLU cc_start: 0.8261 (tt0) cc_final: 0.8055 (tt0)
REVERT: G   71 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.7957 (ptp-110)
REVERT: H   93 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8017 (mm-30)
REVERT: H   95 GLN cc_start: 0.8132 (tt0) cc_final: 0.7270 (tm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 194
  average time/residue: 0.1056
  time to fit residues: 29.6090
Evaluate side-chains
  200 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   89 ASN
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0050
   chunk 85 optimal weight:   20.0000
   chunk 2 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 77 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6196

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.126280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.090318 restraints weight = 34469.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.093530 restraints weight = 17577.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.095683 restraints weight = 11385.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.097052 restraints weight = 8714.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.097891 restraints weight = 7450.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141  12810  Z= 0.213
  Angle     :  0.912  59.199  18535  Z= 0.535
  Chirality :  0.043   0.231   2099
  Planarity :  0.005   0.049   1338
  Dihedral  : 30.708 150.811   4015
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 29.03 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.30), residues: 749
  helix:  1.00 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  33 
 TYR   0.056   0.003   TYR H  83 
 PHE   0.014   0.002   PHE A  84 
 TRP   0.021   0.002   TRP E  47 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.21 (12810)
  covalent geometry    : angle       0.91180 /  0.54 (18535)
  hydrogen bonds       : bond        0.05579 /  3.69 (  745)
  hydrogen bonds       : angle       3.40202 /  2.46 ( 1847)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8231 (ttpp)
REVERT: A  110 TYR cc_start: 0.7343 (t80) cc_final: 0.7027 (t80)
REVERT: B   45 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7081 (tpp80)
REVERT: B   51 TYR cc_start: 0.8107 (m-80) cc_final: 0.7679 (m-80)
REVERT: B   84 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7073 (mtm)
REVERT: C   82 HIS cc_start: 0.8027 (m170) cc_final: 0.7823 (m90)
REVERT: C   92 GLU cc_start: 0.8340 (mp0) cc_final: 0.8016 (pm20)
REVERT: D   48 VAL cc_start: 0.8334 (p) cc_final: 0.8080 (p)
REVERT: E   49 LYS cc_start: 0.9052 (ptmt) cc_final: 0.8411 (ptmt)
REVERT: E   73 GLU cc_start: 0.9065 (tp30) cc_final: 0.8308 (tp30)
REVERT: F   53 GLU cc_start: 0.8111 (tt0) cc_final: 0.7899 (tt0)
REVERT: G   71 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.7953 (ptp-110)
REVERT: H   93 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7882 (mm-30)
REVERT: H   95 GLN cc_start: 0.8153 (tt0) cc_final: 0.7294 (tm-30)
  outliers start: 26
  outliers final: 23
  residues processed: 188
  average time/residue: 0.1102
  time to fit residues: 29.7727
Evaluate side-chains
  198 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 LYS
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 88 optimal weight:   40.0000
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0050
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 80 optimal weight:   30.0000
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.3798

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.126434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.090376 restraints weight = 34003.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.093648 restraints weight = 17323.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.095825 restraints weight = 11193.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.097189 restraints weight = 8541.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.098058 restraints weight = 7297.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141  12810  Z= 0.213
  Angle     :  0.912  59.199  18535  Z= 0.535
  Chirality :  0.043   0.231   2099
  Planarity :  0.005   0.049   1338
  Dihedral  : 30.708 150.811   4015
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 29.03 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.30), residues: 749
  helix:  1.00 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  33 
 TYR   0.056   0.003   TYR H  83 
 PHE   0.014   0.002   PHE A  84 
 TRP   0.021   0.002   TRP E  47 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.21 (12810)
  covalent geometry    : angle       0.91181 /  0.54 (18535)
  hydrogen bonds       : bond        0.05579 /  3.69 (  745)
  hydrogen bonds       : angle       3.40202 /  2.46 ( 1847)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2059.21 seconds
wall clock time: 36 minutes 8.66 seconds (2168.66 seconds total)