Starting phenix.real_space_refine
on Fri Feb 14 04:39:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q15_18060/02_2025/8q15_18060.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q15_18060/02_2025/8q15_18060.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/8q15_18060/02_2025/8q15_18060.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q15_18060/02_2025/8q15_18060.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q15_18060/02_2025/8q15_18060.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q15_18060/02_2025/8q15_18060.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=   0.005 sd=   0.074
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     238      5.49       5
     S      10      5.16       5
     C    5670      2.51       5
     N    1885      2.21       5
     O    2364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10167
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 639
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 3, 'TRANS': 80}
    Chain: "B"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 639
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 3, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 688
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    Chain: "D"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 688
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 3, 'TRANS': 84}
    Chain: "E"
      Number of atoms: 590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 590
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "F"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 792
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "G"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 630
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "H"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "I"
      Number of atoms: 2455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2455
          Classifications: {'DNA': 119}
          Link IDs: {'rna3p': 118}
    Chain: "J"
      Number of atoms: 2424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2424
          Classifications: {'DNA': 119}
          Link IDs: {'rna3p': 118}
  Time building chain proxies: 6.11, per 1000 atoms: 0.60
  Number of scatterers: 10167
  At special positions: 0
  Unit cell: (78.516, 114.866, 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      10     16.00
     P     238     15.00
     O    2364      8.00
     N    1885      7.00
     C    5670      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: 2.58
  Conformation dependent library (CDL) restraints added in 580.2 milliseconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1252

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      78.2% alpha, 2.4% beta
      118 base pairs and 198 stacking pairs defined.
    Time for finding SS restraints: 4.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 39
    Processing helix  chain 'A' and resid 48 through 75
      removed outlier: 3.529A  pdb=" N   ASP A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 92
    Processing helix  chain 'A' and resid 92 through 99
    Processing helix  chain 'B' and resid 28 through 39
    Processing helix  chain 'B' and resid 47 through 75
      removed outlier: 4.256A  pdb=" N   VAL B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 92
      removed outlier: 3.563A  pdb=" N   ASP B  92 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    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 114
    Processing helix  chain 'C' and resid 119 through 131
    Processing helix  chain 'C' and resid 132 through 152
      removed outlier: 3.517A  pdb=" N   ALA C 136 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 78
    Processing helix  chain 'D' and resid 84 through 114
    Processing helix  chain 'D' and resid 119 through 131
    Processing helix  chain 'D' and resid 133 through 152
    Processing helix  chain 'E' and resid 64 through 80
      removed outlier: 3.992A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
      removed outlier: 4.133A  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
      removed outlier: 4.015A  pdb=" N   LEU E 127 " --> pdb=" O   LYS E 123 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG E 132 " --> pdb=" O   ALA E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 58
    Processing helix  chain 'F' and resid 64 through 80
      removed outlier: 4.179A  pdb=" N   ASP F  78 " --> pdb=" O   GLU F  74 " (cutoff:3.500A)
      removed outlier: 4.280A  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 133
      removed outlier: 3.617A  pdb=" N   LEU F 127 " --> pdb=" O   LYS F 123 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG F 132 " --> pdb=" O   ALA F 128 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 30
    Processing helix  chain 'G' and resid 31 through 42
    Processing helix  chain 'G' and resid 50 through 77
      removed outlier: 3.940A  pdb=" N   GLU G  54 " --> pdb=" O   LEU G  50 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ASP G  69 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA G  77 " --> pdb=" O   TYR G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 83 through 94
      removed outlier: 3.544A  pdb=" N   VAL G  87 " --> pdb=" O   THR G  83 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 30
    Processing helix  chain 'H' and resid 31 through 43
    Processing helix  chain 'H' and resid 50 through 77
      removed outlier: 3.903A  pdb=" N   GLU H  54 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP H  69 " --> pdb=" O   ASN H  65 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA H  77 " --> pdb=" O   TYR H  73 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 94
      removed outlier: 3.534A  pdb=" N   VAL H  87 " --> pdb=" O   THR H  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45
      removed outlier: 6.939A  pdb=" N   ARG A  44 " --> pdb=" O   ILE C 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 'B' and resid 44 through 45
      removed outlier: 7.055A  pdb=" N   ARG B  44 " --> pdb=" O   ILE D 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.631A  pdb=" N   ILE B  80 " --> pdb=" O   GLY D  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.826A  pdb=" N   ARG E  84 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA7, first strand: chain 'F' and resid 84 through 85
      removed outlier: 6.670A  pdb=" N   ARG F  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 'F' and resid 119 through 120

    385 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      305 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      118 basepair parallelities
      198 stacking parallelities
  Total time for adding SS restraints: 3.64

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1730
        1.33 -     1.45: 3588
        1.45 -     1.57: 5021
        1.57 -     1.68: 474
        1.68 -     1.80: 18
  Bond restraints: 10831
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" C2   DC J -20 "
       pdb=" O2   DC J -20 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.021 2.00e-02 2.50e+03 1.09e+00
  bond pdb=" CA  ILE G  30 "
       pdb=" CB  ILE G  30 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.07e+00
  bond pdb=" N   PRO B  28 "
       pdb=" CA  PRO B  28 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.05e-01
  bond pdb=" C3'  DG I  64 "
       pdb=" C2'  DG I  64 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.02e-01
  ... (remaining 10826 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 14851
        1.09 -     2.17: 640
        2.17 -     3.26: 139
        3.26 -     4.34: 8
        4.34 -     5.43: 4
  Bond angle restraints: 15642
  Sorted by residual:
  angle pdb=" C4'  DC J -20 "
        pdb=" O4'  DC J -20 "
        pdb=" C1'  DC J -20 "
      ideal   model   delta    sigma   weight residual
     109.70  106.26    3.44 1.50e+00 4.44e-01 5.27e+00
  angle pdb=" C3'  DC I  49 "
        pdb=" C2'  DC I  49 "
        pdb=" C1'  DC I  49 "
      ideal   model   delta    sigma   weight residual
     101.60  104.78   -3.18 1.50e+00 4.44e-01 4.49e+00
  angle pdb=" C3'  DG I  20 "
        pdb=" O3'  DG I  20 "
        pdb=" P    DG I  21 "
      ideal   model   delta    sigma   weight residual
     120.20  123.33   -3.13 1.50e+00 4.44e-01 4.36e+00
  angle pdb=" N   ILE G  30 "
        pdb=" CA  ILE G  30 "
        pdb=" C   ILE G  30 "
      ideal   model   delta    sigma   weight residual
     109.34  105.29    4.05 2.08e+00 2.31e-01 3.79e+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  104.50   -2.90 1.50e+00 4.44e-01 3.74e+00
  ... (remaining 15637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.59: 4749
       33.59 -    67.18: 1109
       67.18 -   100.77: 21
      100.77 -   134.36: 0
      134.36 -   167.95: 1
  Dihedral angle restraints: 5880
    sinusoidal: 3942
      harmonic: 1938
  Sorted by residual:
  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   52.05  167.95     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" N   GLU F  95 "
           pdb=" CA  GLU F  95 "
           pdb=" CB  GLU F  95 "
           pdb=" CG  GLU F  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.76  -58.24     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" CA  ARG D 128 "
           pdb=" CB  ARG D 128 "
           pdb=" CG  ARG D 128 "
           pdb=" CD  ARG D 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.04   57.04     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 5877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1159
       0.026 -    0.052: 457
       0.052 -    0.078: 120
       0.078 -    0.104: 33
       0.104 -    0.130: 18
  Chirality restraints: 1787
  Sorted by residual:
  chirality pdb=" C1'  DC J -20 "
            pdb=" O4'  DC J -20 "
            pdb=" C2'  DC J -20 "
            pdb=" N1   DC J -20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.34    0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  ILE H  47 "
            pdb=" N   ILE H  47 "
            pdb=" C   ILE H  47 "
            pdb=" CB  ILE H  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  ILE H  30 "
            pdb=" N   ILE H  30 "
            pdb=" C   ILE H  30 "
            pdb=" CB  ILE H  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 1784 not shown)

  Planarity restraints: 1151
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J -20 "    0.003 2.00e-02 2.50e+03   2.41e-02 1.31e+01
        pdb=" N1   DC J -20 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J -20 "    0.060 2.00e-02 2.50e+03
        pdb=" O2   DC J -20 "   -0.035 2.00e-02 2.50e+03
        pdb=" N3   DC J -20 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J -20 "    0.010 2.00e-02 2.50e+03
        pdb=" N4   DC J -20 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC J -20 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC J -20 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J -50 "   -0.011 2.00e-02 2.50e+03   1.90e-02 8.16e+00
        pdb=" N1   DC J -50 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DC J -50 "    0.048 2.00e-02 2.50e+03
        pdb=" O2   DC J -50 "   -0.023 2.00e-02 2.50e+03
        pdb=" N3   DC J -50 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DC J -50 "    0.010 2.00e-02 2.50e+03
        pdb=" N4   DC J -50 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5   DC J -50 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J -50 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  21 "   -0.005 2.00e-02 2.50e+03   1.40e-02 5.88e+00
        pdb=" N9   DG I  21 "    0.015 2.00e-02 2.50e+03
        pdb=" C8   DG I  21 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I  21 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DG I  21 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DG I  21 "   -0.016 2.00e-02 2.50e+03
        pdb=" O6   DG I  21 "    0.013 2.00e-02 2.50e+03
        pdb=" N1   DG I  21 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DG I  21 "   -0.033 2.00e-02 2.50e+03
        pdb=" N2   DG I  21 "    0.023 2.00e-02 2.50e+03
        pdb=" N3   DG I  21 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DG I  21 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1148 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 455
        2.71 -     3.26: 9102
        3.26 -     3.80: 19396
        3.80 -     4.35: 23269
        4.35 -     4.90: 33894
  Nonbonded interactions: 86116
  Sorted by model distance:
  nonbonded pdb=" N2   DG I -10 "
            pdb=" O2   DC J  10 "
     model   vdw
     2.160 2.496
  nonbonded pdb=" N2   DG I  -5 "
            pdb=" O2   DC J   5 "
     model   vdw
     2.201 2.496
  nonbonded pdb=" OH  TYR E 100 "
            pdb=" OE1 GLU E 134 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" N1   DG I  -5 "
            pdb=" N3   DC J   5 "
     model   vdw
     2.314 2.560
  nonbonded pdb=" N2   DG I -21 "
            pdb=" O2   DC J  21 "
     model   vdw
     2.319 2.496
  ... (remaining 86111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'G' and resid 26 through 103)
  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:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.140
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10831  Z= 0.166
  Angle     :  0.521   5.426  15642  Z= 0.320
  Chirality :  0.032   0.130   1787
  Planarity :  0.004   0.037   1151
  Dihedral  : 26.645 167.955   4628
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  2.36 %
    Favored  : 96.37 %
  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:  2.99 (0.33), residues: 655
  helix:  2.77 (0.23), residues: 500
  sheet:  None (None), residues: 0
  loop : -0.81 (0.46), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  76 
 PHE   0.009   0.001   PHE D  99 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG G  93 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: F   82 ASP cc_start: 0.6616 (t70) cc_final: 0.6387 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 132
  average time/residue: 0.3800
  time to fit residues: 61.6848
Evaluate side-chains
  83 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain G residue   47 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
B  84 HIS
C  76 GLN
C 113 ASN
C 124 GLN
D  76 GLN
** G  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.189230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.122805 restraints weight = 12499.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.126995 restraints weight = 8465.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127620 restraints weight = 5678.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10831  Z= 0.255
  Angle     :  0.568   5.639  15642  Z= 0.337
  Chirality :  0.034   0.128   1787
  Planarity :  0.004   0.035   1151
  Dihedral  : 30.594 170.692   3328
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  9.62 %
    Favored  : 87.66 %
  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 (0.33), residues: 655
  helix:  2.63 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -0.90 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  78 
 PHE   0.011   0.001   PHE C  94 
 TYR   0.010   0.001   TYR H  52 
 ARG   0.005   0.001   ARG D 128 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.787 
Fit side-chains
REVERT: F   42 PHE cc_start: 0.6395 (m-80) cc_final: 0.6068 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 95
  average time/residue: 0.3002
  time to fit residues: 37.7055
Evaluate side-chains
  90 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   93 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 62 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 71 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** H  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.192375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126796 restraints weight = 12757.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130557 restraints weight = 8469.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.132190 restraints weight = 5802.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10831  Z= 0.176
  Angle     :  0.517   5.423  15642  Z= 0.312
  Chirality :  0.032   0.124   1787
  Planarity :  0.004   0.035   1151
  Dihedral  : 30.480 172.651   3326
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.34 %
    Favored  : 85.30 %
  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:  3.35 (0.33), residues: 655
  helix:  2.99 (0.22), residues: 507
  sheet:  None (None), residues: 0
  loop : -0.73 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  76 
 PHE   0.012   0.001   PHE F  68 
 TYR   0.009   0.001   TYR C 112 
 ARG   0.004   0.000   ARG D 128 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.790 
Fit side-chains
REVERT: B   96 SER cc_start: 0.8576 (t) cc_final: 0.8167 (p)
REVERT: C   67 LYS cc_start: 0.7806 (mttt) cc_final: 0.7296 (tttp)
REVERT: C  101 LYS cc_start: 0.8573 (mttt) cc_final: 0.8350 (mttm)
REVERT: C  145 LYS cc_start: 0.8394 (tttt) cc_final: 0.7935 (mtpt)
REVERT: F   42 PHE cc_start: 0.6428 (m-80) cc_final: 0.6058 (m-10)
REVERT: F   82 ASP cc_start: 0.7408 (t0) cc_final: 0.6967 (t0)
REVERT: G   85 MET cc_start: 0.8296 (mmm) cc_final: 0.8054 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.3659
  time to fit residues: 43.7188
Evaluate side-chains
  92 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   83 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** G  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  26 ASN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.189112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.120906 restraints weight = 12346.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.123798 restraints weight = 9424.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.124597 restraints weight = 7012.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  10831  Z= 0.440
  Angle     :  0.662   7.519  15642  Z= 0.382
  Chirality :  0.039   0.150   1787
  Planarity :  0.005   0.047   1151
  Dihedral  : 30.847 172.385   3323
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 12.52 %
    Favored  : 83.30 %
  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:  2.15 (0.32), residues: 655
  helix:  2.21 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.44 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  76 
 PHE   0.021   0.002   PHE C  94 
 TYR   0.015   0.002   TYR D  66 
 ARG   0.007   0.001   ARG D 128 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7638 (ttp-110)
REVERT: D  117 THR cc_start: 0.8619 (p) cc_final: 0.8396 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 96
  average time/residue: 0.3024
  time to fit residues: 38.0592
Evaluate side-chains
  96 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue   20 SER
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue   93 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  40 HIS
H  26 ASN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.194459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128058 restraints weight = 12155.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.131239 restraints weight = 8831.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.132213 restraints weight = 6491.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10831  Z= 0.197
  Angle     :  0.536   5.551  15642  Z= 0.321
  Chirality :  0.033   0.125   1787
  Planarity :  0.004   0.063   1151
  Dihedral  : 30.527 174.620   3323
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.88 %
    Favored  : 81.67 %
  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:  2.98 (0.33), residues: 655
  helix:  2.81 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.16 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  78 
 PHE   0.013   0.001   PHE F  68 
 TYR   0.009   0.001   TYR A  52 
 ARG   0.008   0.000   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.817 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.7997 (mttt) cc_final: 0.7666 (tttp)
REVERT: C  101 LYS cc_start: 0.8657 (mttt) cc_final: 0.8419 (mttm)
REVERT: C  145 LYS cc_start: 0.8451 (tttt) cc_final: 0.8005 (mtpt)
REVERT: D   81 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (mp)
REVERT: D  117 THR cc_start: 0.8498 (p) cc_final: 0.8272 (p)
REVERT: F   82 ASP cc_start: 0.7314 (t0) cc_final: 0.6906 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 95
  average time/residue: 0.2873
  time to fit residues: 35.9282
Evaluate side-chains
  96 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   83 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.194970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.128622 restraints weight = 12190.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.131812 restraints weight = 8760.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.132796 restraints weight = 6423.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10831  Z= 0.186
  Angle     :  0.528   5.977  15642  Z= 0.317
  Chirality :  0.032   0.128   1787
  Planarity :  0.004   0.055   1151
  Dihedral  : 30.518 175.658   3323
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.34 %
    Favored  : 82.58 %
  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:  3.18 (0.33), residues: 655
  helix:  2.97 (0.22), residues: 507
  sheet:  None (None), residues: 0
  loop : -1.21 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  78 
 PHE   0.012   0.001   PHE F  68 
 TYR   0.010   0.001   TYR C 112 
 ARG   0.006   0.000   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.593 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.7964 (mttt) cc_final: 0.7648 (tttm)
REVERT: C  101 LYS cc_start: 0.8657 (mttt) cc_final: 0.8406 (mttm)
REVERT: C  145 LYS cc_start: 0.8419 (tttt) cc_final: 0.8008 (mtpt)
REVERT: D   81 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: D  117 THR cc_start: 0.8561 (p) cc_final: 0.8340 (p)
REVERT: F   82 ASP cc_start: 0.7358 (t0) cc_final: 0.6945 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 94
  average time/residue: 0.2785
  time to fit residues: 34.5846
Evaluate side-chains
  98 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   93 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 62 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  26 ASN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.190304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123037 restraints weight = 12395.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126069 restraints weight = 9098.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126630 restraints weight = 7005.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  10831  Z= 0.376
  Angle     :  0.622   8.985  15642  Z= 0.362
  Chirality :  0.037   0.147   1787
  Planarity :  0.005   0.057   1151
  Dihedral  : 30.736 175.147   3323
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 14.16 %
    Favored  : 81.31 %
  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:  2.37 (0.32), residues: 655
  helix:  2.40 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.53 (0.48), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  76 
 PHE   0.017   0.002   PHE C  94 
 TYR   0.012   0.002   TYR D  66 
 ARG   0.006   0.001   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.788 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.8005 (mttt) cc_final: 0.7683 (tttm)
REVERT: C  145 LYS cc_start: 0.8504 (tttt) cc_final: 0.8088 (mtpt)
REVERT: D   81 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (mp)
REVERT: D  117 THR cc_start: 0.8635 (p) cc_final: 0.8399 (p)
REVERT: F   82 ASP cc_start: 0.7385 (t0) cc_final: 0.7026 (t0)
  outliers start: 25
  outliers final: 22
  residues processed: 97
  average time/residue: 0.2757
  time to fit residues: 35.7524
Evaluate side-chains
  105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   74 THR
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain H residue   93 ARG
Chi-restraints excluded: chain H residue  101 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.194492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.127399 restraints weight = 12234.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.131377 restraints weight = 8734.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.132120 restraints weight = 6022.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10831  Z= 0.197
  Angle     :  0.544   8.076  15642  Z= 0.323
  Chirality :  0.033   0.177   1787
  Planarity :  0.004   0.046   1151
  Dihedral  : 30.535 177.502   3323
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.52 %
    Favored  : 80.04 %
  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 (0.33), residues: 655
  helix:  2.80 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.12 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G  76 
 PHE   0.012   0.001   PHE F  68 
 TYR   0.008   0.001   TYR A  52 
 ARG   0.006   0.000   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.641 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.7918 (mttt) cc_final: 0.7613 (tttm)
REVERT: C  101 LYS cc_start: 0.8666 (mttt) cc_final: 0.8410 (mttm)
REVERT: C  145 LYS cc_start: 0.8483 (tttt) cc_final: 0.8030 (mtpt)
REVERT: D   81 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8413 (mp)
REVERT: D  117 THR cc_start: 0.8547 (p) cc_final: 0.8321 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 95
  average time/residue: 0.3041
  time to fit residues: 38.0831
Evaluate side-chains
  100 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   50 LEU
Chi-restraints excluded: chain H residue   93 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.194893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.129124 restraints weight = 12225.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.132422 restraints weight = 8950.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.133236 restraints weight = 6293.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10831  Z= 0.184
  Angle     :  0.536   6.578  15642  Z= 0.319
  Chirality :  0.033   0.167   1787
  Planarity :  0.004   0.056   1151
  Dihedral  : 30.538 178.685   3323
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.60 %
    Favored  : 79.31 %
  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:  3.12 (0.33), residues: 655
  helix:  2.92 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.16 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  78 
 PHE   0.012   0.001   PHE F  68 
 TYR   0.012   0.001   TYR C 112 
 ARG   0.008   0.000   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.831 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.7881 (mttt) cc_final: 0.7572 (tttm)
REVERT: C  101 LYS cc_start: 0.8651 (mttt) cc_final: 0.8439 (mttm)
REVERT: C  145 LYS cc_start: 0.8525 (tttt) cc_final: 0.8068 (mtpt)
REVERT: D   81 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (mp)
REVERT: D  117 THR cc_start: 0.8560 (p) cc_final: 0.8330 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 93
  average time/residue: 0.3061
  time to fit residues: 37.2677
Evaluate side-chains
  97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   93 ARG
Chi-restraints excluded: chain H residue  101 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.193244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.127636 restraints weight = 12198.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.130355 restraints weight = 9069.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.131066 restraints weight = 7204.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10831  Z= 0.252
  Angle     :  0.563   6.616  15642  Z= 0.331
  Chirality :  0.034   0.182   1787
  Planarity :  0.004   0.061   1151
  Dihedral  : 30.588 178.804   3323
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.60 %
    Favored  : 79.49 %
  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:  2.90 (0.33), residues: 655
  helix:  2.75 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.25 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  76 
 PHE   0.012   0.001   PHE H 101 
 TYR   0.018   0.002   TYR C 112 
 ARG   0.007   0.000   ARG D 111 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.659 
Fit side-chains
REVERT: C   67 LYS cc_start: 0.7826 (mttt) cc_final: 0.7543 (tttm)
REVERT: C  101 LYS cc_start: 0.8661 (mttt) cc_final: 0.8396 (mttm)
REVERT: C  145 LYS cc_start: 0.8560 (tttt) cc_final: 0.8136 (mtpt)
REVERT: D   81 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8433 (mp)
REVERT: D  117 THR cc_start: 0.8576 (p) cc_final: 0.8342 (p)
REVERT: G   75 GLU cc_start: 0.7735 (tp30) cc_final: 0.7430 (mm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 86
  average time/residue: 0.2760
  time to fit residues: 31.9110
Evaluate side-chains
  92 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain D residue   81 ILE
Chi-restraints excluded: chain D residue  122 GLU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue  125 ILE
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue   47 ILE
Chi-restraints excluded: chain G residue   97 THR
Chi-restraints excluded: chain H residue   93 ARG
Chi-restraints excluded: chain H residue  101 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0270
   chunk 68 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    1.5244

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** H  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.193470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.126064 restraints weight = 12178.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.130129 restraints weight = 8559.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130805 restraints weight = 5793.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10831  Z= 0.235
  Angle     :  0.555   6.596  15642  Z= 0.328
  Chirality :  0.034   0.182   1787
  Planarity :  0.004   0.059   1151
  Dihedral  : 30.587 179.036   3323
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.97 %
    Favored  : 78.95 %
  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 (0.33), residues: 655
  helix:  2.71 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.27 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  76 
 PHE   0.012   0.001   PHE H 101 
 TYR   0.018   0.002   TYR C 112 
 ARG   0.007   0.000   ARG D 111 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2620.56 seconds
wall clock time: 47 minutes 40.99 seconds (2860.99 seconds total)