Starting phenix.real_space_refine
on Tue Jul 29 14:18:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q16_18061/07_2025/8q16_18061.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q16_18061/07_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_18061/07_2025/8q16_18061.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2025/8q16_18061.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2025/8q16_18061.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2025/8q16_18061.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.44, per 1000 atoms: 0.63
  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: 2.87
  Conformation dependent library (CDL) restraints added in 873.6 milliseconds
  

  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: 5.76
  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: 4.71

  Time building geometry restraints manager: 3.43 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:             3.230
  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:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.450
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.870
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (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
 HIS   0.002   0.001   HIS H  76 
 PHE   0.009   0.001   PHE E  42 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG F 117 

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

*********************** 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  : 0.900 
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: 0.4703
  time to fit residues: 68.0813
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  : 1.086 
-------------------------------------------------------------------------------
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 82 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0030
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.9392

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.156136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.103120 restraints weight = 15566.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.105475 restraints weight = 10429.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.107027 restraints weight = 8278.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1184

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= 0.160
  Angle     :  0.531   5.971  18252  Z= 0.321
  Chirality :  0.033   0.127   2087
  Planarity :  0.004   0.032   1280
  Dihedral  : 30.050 179.949   4011
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.67 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.31), residues: 716
  helix:  2.83 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.92 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.009   0.001   PHE E  42 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.006   0.000   ARG F  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04563 (  782)
  hydrogen bonds       : angle       2.77835 ( 1948)
  covalent geometry    : bond        0.00354 (12583)
  covalent geometry    : angle       0.53083 (18252)

*********************** 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
  93 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.8247 (mt) cc_final: 0.8037 (mp)
REVERT: A   26 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7620 (mm110)
REVERT: B  106 SER cc_start: 0.8987 (m) cc_final: 0.8745 (t)
REVERT: D   88 MET cc_start: 0.8251 (tpp) cc_final: 0.7545 (tpp)
REVERT: E   77 GLN cc_start: 0.7889 (tp40) cc_final: 0.7683 (tp40)
  outliers start: 10
  outliers final: 7
  residues processed: 89
  average time/residue: 0.3987
  time to fit residues: 45.2606
Evaluate side-chains
  82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 47 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.155706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.103791 restraints weight = 15781.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105716 restraints weight = 10440.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106361 restraints weight = 8015.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
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= 0.165
  Angle     :  0.532   8.058  18252  Z= 0.319
  Chirality :  0.033   0.130   2087
  Planarity :  0.004   0.031   1280
  Dihedral  : 30.069 179.987   4009
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.00 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.31), residues: 716
  helix:  2.88 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.05 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.018   0.001   PHE C  71 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.007   0.001   ARG D 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 (  782)
  hydrogen bonds       : angle       2.74118 ( 1948)
  covalent geometry    : bond        0.00373 (12583)
  covalent geometry    : angle       0.53237 (18252)

*********************** 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
  92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   26 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7664 (mm110)
REVERT: B  106 SER cc_start: 0.8993 (m) cc_final: 0.8767 (t)
REVERT: D   88 MET cc_start: 0.8288 (tpp) cc_final: 0.7590 (tpp)
REVERT: H   94 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7331 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 88
  average time/residue: 0.3615
  time to fit residues: 41.2402
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  : 0.873 
-------------------------------------------------------------------------------
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 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
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 83 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 70 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 9 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 48 optimal weight:    0.1980
   overall best weight:    1.4984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.154293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.101275 restraints weight = 15739.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103885 restraints weight = 11906.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.104007 restraints weight = 8861.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12583  Z= 0.191
  Angle     :  0.555   8.543  18252  Z= 0.329
  Chirality :  0.034   0.139   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.177 179.765   4009
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.17 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.31), residues: 716
  helix:  2.78 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.08 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.010   0.001   PHE C  94 
 TYR   0.008   0.001   TYR C  66 
 ARG   0.006   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  782)
  hydrogen bonds       : angle       2.79229 ( 1948)
  covalent geometry    : bond        0.00443 (12583)
  covalent geometry    : angle       0.55515 (18252)

*********************** 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
  93 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.846 
Fit side-chains
REVERT: D   88 MET cc_start: 0.8340 (tpp) cc_final: 0.7713 (tpp)
REVERT: H   94 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7244 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.3866
  time to fit residues: 43.6730
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.154964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.102272 restraints weight = 15846.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.104487 restraints weight = 10773.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.105918 restraints weight = 8620.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1879

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= 0.180
  Angle     :  0.544   8.962  18252  Z= 0.324
  Chirality :  0.033   0.137   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.140 179.907   4009
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.17 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.31), residues: 716
  helix:  2.83 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.10 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.009   0.001   PHE E  42 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.005   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  782)
  hydrogen bonds       : angle       2.69468 ( 1948)
  covalent geometry    : bond        0.00413 (12583)
  covalent geometry    : angle       0.54404 (18252)

*********************** 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
  94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8590 (m-40) cc_final: 0.8012 (t0)
REVERT: D   88 MET cc_start: 0.8352 (tpp) cc_final: 0.7563 (tpp)
REVERT: H   94 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7223 (mp10)
  outliers start: 16
  outliers final: 10
  residues processed: 88
  average time/residue: 0.3599
  time to fit residues: 41.1116
Evaluate side-chains
  86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 H residue   50 LEU
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 2 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.157410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106619 restraints weight = 15816.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107510 restraints weight = 14073.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.107813 restraints weight = 12926.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2031

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= 0.167
  Angle     :  0.535   9.472  18252  Z= 0.319
  Chirality :  0.032   0.135   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.088 179.999   4009
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.00 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.04 (0.30), residues: 716
  helix:  2.94 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.07 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.008   0.001   PHE E  42 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.007   0.000   ARG F  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  782)
  hydrogen bonds       : angle       2.63120 ( 1948)
  covalent geometry    : bond        0.00379 (12583)
  covalent geometry    : angle       0.53463 (18252)

*********************** 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
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8572 (m-40) cc_final: 0.8050 (t0)
REVERT: D   88 MET cc_start: 0.8290 (tpp) cc_final: 0.7545 (tpp)
REVERT: H   94 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7198 (mp10)
  outliers start: 15
  outliers final: 12
  residues processed: 86
  average time/residue: 0.3705
  time to fit residues: 41.4361
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  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 78 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.155385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104170 restraints weight = 15877.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.104863 restraints weight = 15435.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105302 restraints weight = 13568.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12583  Z= 0.201
  Angle     :  0.559  10.019  18252  Z= 0.331
  Chirality :  0.034   0.143   2087
  Planarity :  0.004   0.031   1280
  Dihedral  : 30.199 179.919   4009
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.83 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.31), residues: 716
  helix:  2.79 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.16 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  76 
 PHE   0.009   0.001   PHE C  94 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.007   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04752 (  782)
  hydrogen bonds       : angle       2.76857 ( 1948)
  covalent geometry    : bond        0.00468 (12583)
  covalent geometry    : angle       0.55903 (18252)

*********************** 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
  90 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8620 (m-40) cc_final: 0.7863 (t0)
REVERT: D   88 MET cc_start: 0.8376 (tpp) cc_final: 0.7582 (tpp)
REVERT: H   94 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7269 (mp10)
  outliers start: 16
  outliers final: 12
  residues processed: 83
  average time/residue: 0.4139
  time to fit residues: 44.0401
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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 45 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 96 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.155044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.103700 restraints weight = 15842.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.105242 restraints weight = 14460.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105327 restraints weight = 13133.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12583  Z= 0.204
  Angle     :  0.565  11.189  18252  Z= 0.334
  Chirality :  0.034   0.143   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.206 179.995   4009
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.17 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.31), residues: 716
  helix:  2.74 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.24 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  76 
 PHE   0.010   0.001   PHE C  94 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.007   0.001   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04766 (  782)
  hydrogen bonds       : angle       2.77913 ( 1948)
  covalent geometry    : bond        0.00476 (12583)
  covalent geometry    : angle       0.56473 (18252)

*********************** 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
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8620 (m-40) cc_final: 0.7882 (t0)
REVERT: D   88 MET cc_start: 0.8396 (tpp) cc_final: 0.7752 (tpp)
REVERT: H   94 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7319 (mp10)
  outliers start: 16
  outliers final: 13
  residues processed: 84
  average time/residue: 0.4687
  time to fit residues: 51.4853
Evaluate side-chains
  85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 H residue   50 LEU
Chi-restraints excluded: chain H residue   74 THR
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 92 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 25 optimal weight:    0.3980
   chunk 77 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.156496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.105604 restraints weight = 15802.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106640 restraints weight = 14305.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.107116 restraints weight = 12883.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12583  Z= 0.173
  Angle     :  0.541  11.334  18252  Z= 0.322
  Chirality :  0.033   0.135   2087
  Planarity :  0.004   0.030   1280
  Dihedral  : 30.083 179.763   4009
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.31), residues: 716
  helix:  2.91 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.19 (0.41), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.008   0.001   PHE E  42 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.007   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  782)
  hydrogen bonds       : angle       2.64617 ( 1948)
  covalent geometry    : bond        0.00393 (12583)
  covalent geometry    : angle       0.54146 (18252)

*********************** 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
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 1.566 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8571 (m-40) cc_final: 0.7902 (t0)
REVERT: D   88 MET cc_start: 0.8336 (tpp) cc_final: 0.7558 (tpp)
REVERT: F   69 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7902 (mt0)
REVERT: H   94 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7315 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 83
  average time/residue: 0.4519
  time to fit residues: 48.4418
Evaluate side-chains
  88 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  144 THR
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   69 GLN
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 5 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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**
D  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.155828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.104877 restraints weight = 15602.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.105662 restraints weight = 14453.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.106235 restraints weight = 13037.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12583  Z= 0.186
  Angle     :  0.554  11.935  18252  Z= 0.328
  Chirality :  0.033   0.138   2087
  Planarity :  0.004   0.029   1280
  Dihedral  : 30.118 179.851   4009
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.00 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.31), residues: 716
  helix:  2.82 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.23 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.008   0.001   PHE C  94 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.007   0.001   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04577 (  782)
  hydrogen bonds       : angle       2.70878 ( 1948)
  covalent geometry    : bond        0.00430 (12583)
  covalent geometry    : angle       0.55444 (18252)

********************** 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
  89 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8581 (m-40) cc_final: 0.7907 (t0)
REVERT: D   88 MET cc_start: 0.8367 (tpp) cc_final: 0.7578 (tpp)
REVERT: F   69 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7747 (mt0)
REVERT: H   94 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7335 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 83
  average time/residue: 0.3613
  time to fit residues: 38.8233
Evaluate side-chains
  87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue  152 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  144 THR
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   69 GLN
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 84 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 56 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.157799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108722 restraints weight = 15682.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.109034 restraints weight = 16451.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.109450 restraints weight = 14740.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2414

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= 0.155
  Angle     :  0.529  11.537  18252  Z= 0.316
  Chirality :  0.032   0.133   2087
  Planarity :  0.004   0.029   1280
  Dihedral  : 29.993 179.551   4009
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.00 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.31), residues: 716
  helix:  3.02 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.15 (0.40), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 114 
 PHE   0.007   0.001   PHE E  42 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.007   0.000   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  782)
  hydrogen bonds       : angle       2.55929 ( 1948)
  covalent geometry    : bond        0.00343 (12583)
  covalent geometry    : angle       0.52917 (18252)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4516.24 seconds
wall clock time: 82 minutes 11.30 seconds (4931.30 seconds total)