Starting phenix.real_space_refine
on Sat Aug 23 10:18:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2025/8q16_18061.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      13      5.16       5
     C    6516      2.51       5
     N    2175      2.21       5
     O    2775      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11773
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 776
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "B"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 763
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "C"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 733
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "D"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 710
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 776
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 737
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 737
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "G"
      Number of atoms: 628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 628
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "H"
      Number of atoms: 623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 623
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 2.47, per 1000 atoms: 0.21
  Number of scatterers: 11773
  At special positions: 0
  Unit cell: (74.881, 124.317, 118.501, 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      13     16.00
     P     294     15.00
     O    2775      8.00
     N    2175      7.00
     C    6516      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: 1.14
  Conformation dependent library (CDL) restraints added in 344.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1362

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      75.7% alpha, 2.7% beta
      147 base pairs and 240 stacking pairs defined.
    Time for finding SS restraints: 1.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 24
    Processing helix  chain 'A' and resid 28 through 39
    Processing helix  chain 'A' and resid 47 through 75
      removed outlier: 4.585A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 92
      removed outlier: 3.575A  pdb=" N   ASP A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 99
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'B' and resid 19 through 24
    Processing helix  chain 'B' and resid 28 through 39
    Processing helix  chain 'B' and resid 48 through 75
    Processing helix  chain 'B' and resid 81 through 92
    Processing helix  chain 'B' and resid 92 through 99
    Processing helix  chain 'C' and resid 66 through 78
    Processing helix  chain 'C' and resid 84 through 113
    Processing helix  chain 'C' and resid 119 through 131
    Processing helix  chain 'C' and resid 133 through 152
      removed outlier: 3.651A  pdb=" N   SER C 152 " --> pdb=" O   THR C 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 78
    Processing helix  chain 'D' and resid 84 through 113
    Processing helix  chain 'D' and resid 119 through 131
    Processing helix  chain 'D' and resid 133 through 153
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 3.647A  pdb=" N   LEU E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 80
      removed outlier: 4.057A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   PHE E  79 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 133
    Processing helix  chain 'F' and resid 46 through 58
    Processing helix  chain 'F' and resid 64 through 80
      removed outlier: 4.016A  pdb=" N   ASP F  78 " --> pdb=" O   GLU F  74 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   PHE F  79 " --> pdb=" O   ILE F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 115
    Processing helix  chain 'F' and resid 121 through 132
    Processing helix  chain 'G' and resid 25 through 30
      removed outlier: 4.006A  pdb=" N   GLN G  28 " --> pdb=" O   GLY G  25 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 31 through 42
    Processing helix  chain 'G' and resid 50 through 77
      removed outlier: 3.804A  pdb=" N   GLU G  54 " --> pdb=" O   LEU G  50 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ARG G  56 " --> pdb=" O   TYR G  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 83 through 94
      removed outlier: 3.537A  pdb=" N   GLN G  94 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 30
      removed outlier: 3.719A  pdb=" N   GLN H  28 " --> pdb=" O   GLY H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 42
      removed outlier: 3.535A  pdb=" N   ILE H  35 " --> pdb=" O   ALA H  31 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 77
      removed outlier: 3.963A  pdb=" N   GLU H  54 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45
      removed outlier: 7.316A  pdb=" N   ARG A  44 " --> pdb=" O   ILE D 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
    Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104
      removed outlier: 7.187A  pdb=" N   THR A 103 " --> pdb=" O   TYR H  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45
      removed outlier: 7.250A  pdb=" N   ARG B  44 " --> pdb=" O   ILE C 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 80
    Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 104
      removed outlier: 6.942A  pdb=" N   THR B 103 " --> pdb=" O   TYR G  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.777A  pdb=" N   ARG E  84 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85
      removed outlier: 7.022A  pdb=" N   ARG F  84 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120

    406 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      748 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      240 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 1.48 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: 1894
        1.33 -     1.45: 4330
        1.45 -     1.57: 5749
        1.57 -     1.68: 586
        1.68 -     1.80: 24
  Bond restraints: 12583
  Sorted by residual:
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" C3'  DT J  14 "
       pdb=" C2'  DT J  14 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 9.84e-01
  bond pdb=" CB  PRO E  44 "
       pdb=" CG  PRO E  44 "
    ideal  model  delta    sigma   weight residual
    1.492  1.541 -0.049 5.00e-02 4.00e+02 9.61e-01
  bond pdb=" C4'  DT J  -6 "
       pdb=" O4'  DT J  -6 "
    ideal  model  delta    sigma   weight residual
    1.450  1.432  0.018 2.00e-02 2.50e+03 8.16e-01
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.449 -0.027 3.00e-02 1.11e+03 7.92e-01
  ... (remaining 12578 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 17308
        1.11 -     2.22: 772
        2.22 -     3.33: 157
        3.33 -     4.44: 7
        4.44 -     5.55: 8
  Bond angle restraints: 18252
  Sorted by residual:
  angle pdb=" C   ARG E  41 "
        pdb=" CA  ARG E  41 "
        pdb=" CB  ARG E  41 "
      ideal   model   delta    sigma   weight residual
     110.42  115.09   -4.67 1.99e+00 2.53e-01 5.50e+00
  angle pdb=" C3'  DG I   2 "
        pdb=" C2'  DG I   2 "
        pdb=" C1'  DG I   2 "
      ideal   model   delta    sigma   weight residual
     101.60  104.66   -3.06 1.50e+00 4.44e-01 4.16e+00
  angle pdb=" CA  VAL F 118 "
        pdb=" C   VAL F 118 "
        pdb=" N   THR F 119 "
      ideal   model   delta    sigma   weight residual
     116.60  119.40   -2.80 1.45e+00 4.76e-01 3.72e+00
  angle pdb=" C3'  DG I  -5 "
        pdb=" C2'  DG I  -5 "
        pdb=" C1'  DG I  -5 "
      ideal   model   delta    sigma   weight residual
     101.60   98.76    2.84 1.50e+00 4.44e-01 3.59e+00
  angle pdb=" C3'  DC I   1 "
        pdb=" C2'  DC I   1 "
        pdb=" C1'  DC I   1 "
      ideal   model   delta    sigma   weight residual
     101.60  104.43   -2.83 1.50e+00 4.44e-01 3.57e+00
  ... (remaining 18247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 5560
       35.95 -    71.90: 1215
       71.90 -   107.85: 8
      107.85 -   143.80: 2
      143.80 -   179.75: 1
  Dihedral angle restraints: 6786
    sinusoidal: 4674
      harmonic: 2112
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.75 -179.75     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.92  138.08     1      3.50e+01 8.16e-04 1.37e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   86.16  133.84     1      3.50e+01 8.16e-04 1.33e+01
  ... (remaining 6783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1312
       0.027 -    0.053: 576
       0.053 -    0.080: 141
       0.080 -    0.107: 38
       0.107 -    0.134: 20
  Chirality restraints: 2087
  Sorted by residual:
  chirality pdb=" CA  ILE C 118 "
            pdb=" N   ILE C 118 "
            pdb=" C   ILE C 118 "
            pdb=" CB  ILE C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  PRO G  33 "
            pdb=" N   PRO G  33 "
            pdb=" C   PRO G  33 "
            pdb=" CB  PRO G  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE D 118 "
            pdb=" N   ILE D 118 "
            pdb=" C   ILE D 118 "
            pdb=" CB  ILE D 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 2084 not shown)

  Planarity restraints: 1280
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -13 "    0.021 2.00e-02 2.50e+03   9.23e-03 2.34e+00
        pdb=" N9   DA I -13 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DA I -13 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -13 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -13 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -13 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -13 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -13 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -13 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "   -0.022 2.00e-02 2.50e+03   8.94e-03 2.20e+00
        pdb=" N9   DA I  47 "    0.016 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 131 "   -0.024 5.00e-02 4.00e+02   3.66e-02 2.14e+00
        pdb=" N   PRO D 132 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1277 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 746
        2.72 -     3.27: 10591
        3.27 -     3.81: 23042
        3.81 -     4.36: 26420
        4.36 -     4.90: 38709
  Nonbonded interactions: 99508
  Sorted by model distance:
  nonbonded pdb=" N2   DG I -10 "
            pdb=" O2   DC J  10 "
     model   vdw
     2.181 2.496
  nonbonded pdb=" OG1 THR E 119 "
            pdb=" NH1 ARG H  46 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OG1 THR G  74 "
            pdb=" OD2 ASP G  86 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   SER A  18 "
            pdb=" OG  SER A  21 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" NH2 ARG B  34 "
            pdb=" OE1 GLU C  64 "
     model   vdw
     2.307 3.120
  ... (remaining 99503 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 18 through 118)
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 63 through 152)
  selection = (chain 'D' and resid 63 through 152)
}
ncs_group {
  reference = (chain 'E' and resid 45 through 134)
  selection = (chain 'F' and resid 45 through 134)
}
ncs_group {
  reference = (chain 'G' and resid 25 through 102)
  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:             3.540
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.400
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12583  Z= 0.194
  Angle     :  0.545   5.553  18252  Z= 0.327
  Chirality :  0.033   0.134   2087
  Planarity :  0.004   0.037   1280
  Dihedral  : 26.753 179.755   5424
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  2.50 %
    Favored  : 97.00 %
  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 aren not related in a simple way.
  whole:  2.53 (0.31), residues: 716
  helix:  2.56 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.03 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 117 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.009   0.001   PHE E  42 
 HIS   0.002   0.001   HIS H  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12583)
  covalent geometry    : angle       0.54476 (18252)
  hydrogen bonds       : bond        0.11397 (  782)
  hydrogen bonds       : angle       3.74409 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.8403 (mt) cc_final: 0.7918 (mt)
REVERT: A   26 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7809 (mm110)
REVERT: B   77 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8476 (ttmm)
REVERT: B  106 SER cc_start: 0.9147 (m) cc_final: 0.8764 (t)
REVERT: B  112 ASN cc_start: 0.8459 (t0) cc_final: 0.7993 (p0)
REVERT: D   75 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8543 (mmtm)
REVERT: D   88 MET cc_start: 0.8337 (tpp) cc_final: 0.7646 (tpp)
REVERT: F   74 GLU cc_start: 0.7919 (tt0) cc_final: 0.7671 (tt0)
REVERT: H   98 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt)
  outliers start: 3
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2135
  time to fit residues: 31.0612
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   98 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C 113 ASN
C 124 GLN
D  78 HIS
D 124 GLN
E  69 GLN
** G  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  76 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.156818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.103946 restraints weight = 15681.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106312 restraints weight = 10399.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107866 restraints weight = 8247.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108724 restraints weight = 7286.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.108885 restraints weight = 6816.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12583  Z= 0.151
  Angle     :  0.522   5.742  18252  Z= 0.316
  Chirality :  0.032   0.130   2087
  Planarity :  0.004   0.032   1280
  Dihedral  : 30.011 179.850   4011
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.17 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.31), residues: 716
  helix:  2.88 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.85 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  53 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.009   0.001   PHE E  42 
 HIS   0.003   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12583)
  covalent geometry    : angle       0.52171 (18252)
  hydrogen bonds       : bond        0.04515 (  782)
  hydrogen bonds       : angle       2.74129 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   26 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7618 (mm110)
REVERT: B  106 SER cc_start: 0.8968 (m) cc_final: 0.8721 (t)
REVERT: D   88 MET cc_start: 0.8204 (tpp) cc_final: 0.7523 (tpp)
REVERT: E   77 GLN cc_start: 0.7876 (tp40) cc_final: 0.7670 (tp40)
REVERT: F   53 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7877 (mtt90)
  outliers start: 8
  outliers final: 6
  residues processed: 87
  average time/residue: 0.1923
  time to fit residues: 21.0591
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   83 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 84 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
G  76 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.156348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.103403 restraints weight = 15827.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.105745 restraints weight = 10457.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107311 restraints weight = 8306.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108007 restraints weight = 7330.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108007 restraints weight = 6878.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12583  Z= 0.159
  Angle     :  0.527   7.359  18252  Z= 0.317
  Chirality :  0.032   0.129   2087
  Planarity :  0.004   0.031   1280
  Dihedral  : 30.034 179.943   4009
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.50 %
    Favored  : 87.83 %
  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 aren not related in a simple way.
  whole:  3.09 (0.31), residues: 716
  helix:  2.95 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.97 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 128 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.015   0.001   PHE C  71 
 HIS   0.003   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12583)
  covalent geometry    : angle       0.52697 (18252)
  hydrogen bonds       : bond        0.04466 (  782)
  hydrogen bonds       : angle       2.71386 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   26 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7545 (mm110)
REVERT: B  106 SER cc_start: 0.8967 (m) cc_final: 0.8744 (t)
REVERT: D   88 MET cc_start: 0.8226 (tpp) cc_final: 0.7547 (tpp)
REVERT: H   94 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7240 (mp10)
  outliers start: 10
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1610
  time to fit residues: 18.7978
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue   94 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.157557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.106587 restraints weight = 15745.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108277 restraints weight = 10339.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109226 restraints weight = 8031.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109520 restraints weight = 8144.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109599 restraints weight = 7368.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12583  Z= 0.144
  Angle     :  0.512   8.812  18252  Z= 0.309
  Chirality :  0.032   0.126   2087
  Planarity :  0.004   0.031   1280
  Dihedral  : 29.975 179.774   4009
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.83 %
    Favored  : 86.33 %
  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 aren not related in a simple way.
  whole:  3.30 (0.30), residues: 716
  helix:  3.07 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.77 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  53 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.008   0.001   PHE E  42 
 HIS   0.003   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (12583)
  covalent geometry    : angle       0.51241 (18252)
  hydrogen bonds       : bond        0.04187 (  782)
  hydrogen bonds       : angle       2.55007 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7796 (mp) cc_final: 0.7334 (mp)
REVERT: A   26 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7454 (mm110)
REVERT: A   75 ASN cc_start: 0.8559 (m-40) cc_final: 0.7968 (t0)
REVERT: B  106 SER cc_start: 0.8920 (m) cc_final: 0.8689 (t)
REVERT: D   88 MET cc_start: 0.8189 (tpp) cc_final: 0.7518 (tpp)
REVERT: E  124 ASP cc_start: 0.7918 (m-30) cc_final: 0.7593 (m-30)
REVERT: H   94 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7193 (mp10)
  outliers start: 11
  outliers final: 6
  residues processed: 91
  average time/residue: 0.1531
  time to fit residues: 17.8706
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   94 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0270
   chunk 31 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.2042

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.156122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.104789 restraints weight = 15879.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.106700 restraints weight = 10564.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.107199 restraints weight = 8442.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107554 restraints weight = 8090.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107606 restraints weight = 7582.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12583  Z= 0.173
  Angle     :  0.536   5.464  18252  Z= 0.320
  Chirality :  0.033   0.137   2087
  Planarity :  0.004   0.029   1280
  Dihedral  : 30.108 179.944   4009
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.83 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.16 (0.31), residues: 716
  helix:  2.96 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.79 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 129 
 TYR   0.008   0.001   TYR B  59 
 PHE   0.009   0.001   PHE E  42 
 HIS   0.003   0.001   HIS H  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12583)
  covalent geometry    : angle       0.53553 (18252)
  hydrogen bonds       : bond        0.04575 (  782)
  hydrogen bonds       : angle       2.69776 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7941 (mp) cc_final: 0.7361 (mp)
REVERT: A   26 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7523 (mm110)
REVERT: A   75 ASN cc_start: 0.8591 (m-40) cc_final: 0.8021 (t0)
REVERT: D   88 MET cc_start: 0.8303 (tpp) cc_final: 0.7754 (tpp)
REVERT: F   95 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7248 (tp30)
REVERT: H   94 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7248 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1861
  time to fit residues: 21.2727
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   95 GLU
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue   94 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 26 optimal weight:    0.1980
   chunk 97 optimal weight:   20.0000
   chunk 4 optimal weight:    0.6980
   chunk 74 optimal weight:    7.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.160453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111036 restraints weight = 15806.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.112412 restraints weight = 13842.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112847 restraints weight = 12689.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112999 restraints weight = 11285.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.113435 restraints weight = 10523.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12583  Z= 0.139
  Angle     :  0.506   5.788  18252  Z= 0.307
  Chirality :  0.031   0.127   2087
  Planarity :  0.003   0.031   1280
  Dihedral  : 29.931 179.586   4009
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 15.33 %
    Favored  : 83.83 %
  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 aren not related in a simple way.
  whole:  3.43 (0.30), residues: 716
  helix:  3.17 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.73 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 129 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.007   0.001   PHE E  42 
 HIS   0.002   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12583)
  covalent geometry    : angle       0.50605 (18252)
  hydrogen bonds       : bond        0.04093 (  782)
  hydrogen bonds       : angle       2.43493 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7672 (mp) cc_final: 0.7178 (mp)
REVERT: A   26 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7433 (mm110)
REVERT: A   75 ASN cc_start: 0.8489 (m-40) cc_final: 0.8076 (t0)
REVERT: E  124 ASP cc_start: 0.7719 (m-30) cc_final: 0.7441 (m-30)
REVERT: G   93 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8483 (mmm160)
REVERT: H   94 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7235 (mp10)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1949
  time to fit residues: 20.8071
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   94 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
D 124 GLN
E  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.150628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.097683 restraints weight = 15962.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.100493 restraints weight = 11674.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.100710 restraints weight = 8475.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.100891 restraints weight = 8575.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.100972 restraints weight = 8192.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12583  Z= 0.258
  Angle     :  0.603   7.633  18252  Z= 0.352
  Chirality :  0.036   0.159   2087
  Planarity :  0.004   0.031   1280
  Dihedral  : 30.343 179.608   4009
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.83 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.31), residues: 716
  helix:  2.72 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 129 
 TYR   0.011   0.002   TYR C  66 
 PHE   0.011   0.002   PHE D 150 
 HIS   0.004   0.001   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (12583)
  covalent geometry    : angle       0.60330 (18252)
  hydrogen bonds       : bond        0.05245 (  782)
  hydrogen bonds       : angle       2.95147 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASN cc_start: 0.8667 (m-40) cc_final: 0.7889 (t0)
REVERT: F   95 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7324 (tp30)
REVERT: F  121 MET cc_start: 0.7566 (mtp) cc_final: 0.7356 (mtp)
REVERT: H   94 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7286 (mp10)
  outliers start: 18
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1754
  time to fit residues: 20.4083
Evaluate side-chains
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   95 GLU
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   94 GLN
Chi-restraints excluded: chain H residue   97 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
E  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.154775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.103963 restraints weight = 15738.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.104341 restraints weight = 17293.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.104924 restraints weight = 15240.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105178 restraints weight = 14212.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.105320 restraints weight = 12928.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12583  Z= 0.222
  Angle     :  0.582  12.285  18252  Z= 0.341
  Chirality :  0.035   0.146   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.277 179.912   4009
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.17 %
    Favored  : 82.00 %
  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 aren not related in a simple way.
  whole:  2.61 (0.30), residues: 716
  helix:  2.62 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.23 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 129 
 TYR   0.009   0.001   TYR D  66 
 PHE   0.011   0.001   PHE C  94 
 HIS   0.004   0.001   HIS H  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (12583)
  covalent geometry    : angle       0.58170 (18252)
  hydrogen bonds       : bond        0.04884 (  782)
  hydrogen bonds       : angle       2.83516 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8614 (m-40) cc_final: 0.7892 (t0)
REVERT: H   94 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7348 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1715
  time to fit residues: 19.0206
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain G residue   78 ARG
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   94 GLN
Chi-restraints excluded: chain H residue   97 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.156274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.105420 restraints weight = 15631.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.107066 restraints weight = 13400.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107421 restraints weight = 11424.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.107523 restraints weight = 10852.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107758 restraints weight = 10168.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12583  Z= 0.179
  Angle     :  0.556  12.360  18252  Z= 0.327
  Chirality :  0.033   0.136   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.136 179.867   4009
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.33 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.30), residues: 716
  helix:  2.82 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.19 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 129 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.008   0.001   PHE E  42 
 HIS   0.003   0.001   HIS H  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12583)
  covalent geometry    : angle       0.55588 (18252)
  hydrogen bonds       : bond        0.04516 (  782)
  hydrogen bonds       : angle       2.69553 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8585 (m-40) cc_final: 0.7886 (t0)
REVERT: D   88 MET cc_start: 0.8543 (tpp) cc_final: 0.8271 (mmm)
REVERT: H   94 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7357 (mp10)
  outliers start: 13
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1781
  time to fit residues: 18.4275
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   94 GLN
Chi-restraints excluded: chain H residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109906 restraints weight = 15825.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111552 restraints weight = 13817.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111835 restraints weight = 11686.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.112140 restraints weight = 11256.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112530 restraints weight = 10220.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12583  Z= 0.146
  Angle     :  0.529  11.975  18252  Z= 0.313
  Chirality :  0.031   0.127   2087
  Planarity :  0.004   0.029   1280
  Dihedral  : 29.908 179.467   4009
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.33 %
    Favored  : 81.83 %
  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 aren not related in a simple way.
  whole:  3.25 (0.30), residues: 716
  helix:  3.09 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.99 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 129 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.006   0.001   PHE F  68 
 HIS   0.003   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12583)
  covalent geometry    : angle       0.52925 (18252)
  hydrogen bonds       : bond        0.04086 (  782)
  hydrogen bonds       : angle       2.48408 ( 1948)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8451 (m-40) cc_final: 0.7922 (t0)
REVERT: G   93 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8532 (mmm160)
  outliers start: 11
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1750
  time to fit residues: 17.9821
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0670
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
D  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.111088 restraints weight = 15701.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111639 restraints weight = 16440.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.112271 restraints weight = 14975.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112516 restraints weight = 13958.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.113349 restraints weight = 12667.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12583  Z= 0.146
  Angle     :  0.535  11.864  18252  Z= 0.315
  Chirality :  0.031   0.129   2087
  Planarity :  0.004   0.039   1280
  Dihedral  : 29.930 179.420   4009
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.50 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.30 (0.30), residues: 716
  helix:  3.11 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.94 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  53 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.007   0.001   PHE E  42 
 HIS   0.004   0.001   HIS F 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12583)
  covalent geometry    : angle       0.53516 (18252)
  hydrogen bonds       : bond        0.04102 (  782)
  hydrogen bonds       : angle       2.48822 ( 1948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1765.68 seconds
wall clock time: 31 minutes 13.37 seconds (1873.37 seconds total)