Starting phenix.real_space_refine
on Sun Jan 19 12:48:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vfy_43194/01_2025/8vfy_43194.cif"
  }
  resolution = 2.89
  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=   0.000 sd=   0.001
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     342      5.49       5
     S      21      5.16       5
     C    7786      2.51       5
     N    2611      2.21       5
     O    3286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 14046
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 927
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3501
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "J"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3510
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "O"
      Number of atoms: 856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 856
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 7, 'TRANS': 94}
  Time building chain proxies: 7.74, per 1000 atoms: 0.55
  Number of scatterers: 14046
  At special positions: 0
  Unit cell: (84.48, 118.8, 192.72, 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      21     16.00
     P     342     15.00
     O    3286      8.00
     N    2611      7.00
     C    7786      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: 3.34
  Conformation dependent library (CDL) restraints added in 989.8 milliseconds
  

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 11 sheets defined
      68.1% alpha, 3.2% beta
      171 base pairs and 306 stacking pairs defined.
    Time for finding SS restraints: 6.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.618A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 40
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.742A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.370A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.549A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.537A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.809A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.637A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.507A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.323A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.527A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
      removed outlier: 3.561A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL H 111 " --> pdb=" O   ALA H 107 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 174 through 186
    Processing helix  chain 'O' and resid 192 through 204
    Processing helix  chain 'O' and resid 205 through 209
      removed outlier: 3.690A  pdb=" N   GLN O 209 " --> pdb=" O   TYR O 206 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 210 through 225
      removed outlier: 4.029A  pdb=" N   TRP O 214 " --> pdb=" O   ASN O 210 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.804A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.521A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.486A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.723A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.520A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.468A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231

    436 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      417 hydrogen bonds
      834 hydrogen bond angles
      0 basepair planarities
      171 basepair parallelities
      306 stacking parallelities
  Total time for adding SS restraints: 5.31

  Time building geometry restraints manager: 3.94 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: 2566
        1.33 -     1.45: 4879
        1.45 -     1.57: 6846
        1.57 -     1.69: 682
        1.69 -     1.81: 35
  Bond restraints: 15008
  Sorted by residual:
  bond pdb=" N   HIS O 168 "
       pdb=" CA  HIS O 168 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" N   LYS D  30 "
       pdb=" CA  LYS D  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" N   ALA C  10 "
       pdb=" CA  ALA C  10 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   LYS H  30 "
       pdb=" CA  LYS H  30 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   LYS B  20 "
       pdb=" CA  LYS B  20 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  ... (remaining 15003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 20049
        1.17 -     2.33: 1297
        2.33 -     3.50: 345
        3.50 -     4.66: 34
        4.66 -     5.83: 6
  Bond angle restraints: 21731
  Sorted by residual:
  angle pdb=" C2'  DT J  55 "
        pdb=" C1'  DT J  55 "
        pdb=" N1   DT J  55 "
      ideal   model   delta    sigma   weight residual
     113.50  117.99   -4.49 1.50e+00 4.44e-01 8.98e+00
  angle pdb=" C2'  DT I 140 "
        pdb=" C1'  DT I 140 "
        pdb=" N1   DT I 140 "
      ideal   model   delta    sigma   weight residual
     113.50  117.92   -4.42 1.50e+00 4.44e-01 8.69e+00
  angle pdb=" C2'  DC I 110 "
        pdb=" C1'  DC I 110 "
        pdb=" N1   DC I 110 "
      ideal   model   delta    sigma   weight residual
     113.50  117.76   -4.26 1.50e+00 4.44e-01 8.07e+00
  angle pdb=" C2'  DT I 161 "
        pdb=" C1'  DT I 161 "
        pdb=" N1   DT I 161 "
      ideal   model   delta    sigma   weight residual
     113.50  117.59   -4.09 1.50e+00 4.44e-01 7.43e+00
  angle pdb=" C2'  DT I  69 "
        pdb=" C1'  DT I  69 "
        pdb=" N1   DT I  69 "
      ideal   model   delta    sigma   weight residual
     113.50  117.55   -4.05 1.50e+00 4.44e-01 7.29e+00
  ... (remaining 21726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.36: 6504
       31.36 -    62.73: 1665
       62.73 -    94.09: 52
       94.09 -   125.46: 0
      125.46 -   156.82: 2
  Dihedral angle restraints: 8223
    sinusoidal: 5666
      harmonic: 2557
  Sorted by residual:
  dihedral pdb=" C4'  DG J 127 "
           pdb=" C3'  DG J 127 "
           pdb=" O3'  DG J 127 "
           pdb=" P    DG J 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.18  156.82     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" C4'  DC J  93 "
           pdb=" C3'  DC J  93 "
           pdb=" O3'  DC J  93 "
           pdb=" P    DC J  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.58  151.42     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  LYS O 237 "
           pdb=" C   LYS O 237 "
           pdb=" N   PRO O 238 "
           pdb=" CA  PRO O 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.38   17.62     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1616
       0.032 -    0.064: 525
       0.064 -    0.095: 263
       0.095 -    0.127: 38
       0.127 -    0.159: 5
  Chirality restraints: 2447
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  ILE G 111 "
            pdb=" N   ILE G 111 "
            pdb=" C   ILE G 111 "
            pdb=" CB  ILE G 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 2444 not shown)

  Planarity restraints: 1565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS O 237 "   -0.048 5.00e-02 4.00e+02   7.30e-02 8.53e+00
        pdb=" N   PRO O 238 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO O 238 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO O 238 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I 140 "    0.038 2.00e-02 2.50e+03   1.78e-02 7.88e+00
        pdb=" N1   DT I 140 "   -0.036 2.00e-02 2.50e+03
        pdb=" C2   DT I 140 "   -0.008 2.00e-02 2.50e+03
        pdb=" O2   DT I 140 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT I 140 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DT I 140 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT I 140 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT I 140 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I 140 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT I 140 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO O 171 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO O 172 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO O 172 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO O 172 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1562 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1294
        2.74 -     3.28: 12610
        3.28 -     3.82: 27731
        3.82 -     4.36: 32977
        4.36 -     4.90: 47101
  Nonbonded interactions: 121713
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR B  72 "
            pdb=" OE2 GLU D  76 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR F  72 "
            pdb=" OE2 GLU H  76 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.275 3.040
  ... (remaining 121708 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 118)
}
ncs_group {
  reference = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:         0.090
  Set scattering table:                    0.130
  Process input model:                     35.840
  Find NCS groups from input model:        0.270
  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:10.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.005   0.047  15008  Z= 0.254
  Angle     :  0.678   5.829  21731  Z= 0.427
  Chirality :  0.039   0.159   2447
  Planarity :  0.005   0.073   1565
  Dihedral  : 26.421 156.825   6575
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.74 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.21 %
    Favored  : 98.52 %
  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:  2.05 (0.29), residues: 863
  helix:  2.21 (0.22), residues: 577
  sheet: -1.65 (1.37), residues: 12
  loop : -0.34 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP O 214 
 HIS   0.003   0.001   HIS D  49 
 PHE   0.007   0.001   PHE E 104 
 TYR   0.007   0.001   TYR G  57 
 ARG   0.003   0.000   ARG E  42 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8872 (p) cc_final: 0.8313 (t)
REVERT: A   76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7704 (mt0)
REVERT: B   85 ASP cc_start: 0.9143 (m-30) cc_final: 0.8911 (m-30)
REVERT: C   90 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0)
REVERT: C   95 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9063 (tttm)
REVERT: D  108 LYS cc_start: 0.8240 (ptmm) cc_final: 0.8016 (ptpp)
REVERT: E   79 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8520 (mtpm)
REVERT: G  120 THR cc_start: 0.8473 (p) cc_final: 0.8052 (p)
REVERT: H   59 MET cc_start: 0.9127 (tpp) cc_final: 0.8898 (tpt)
REVERT: H  113 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8341 (tt0)
REVERT: H  115 THR cc_start: 0.9240 (m) cc_final: 0.9030 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 186
  average time/residue: 1.8603
  time to fit residues: 368.6991
Evaluate side-chains
  117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   88 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
D  47 GLN
E  68 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.105692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.069628 restraints weight = 35697.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.08
r_work: 0.3117 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15008  Z= 0.254
  Angle     :  0.615   6.564  21731  Z= 0.370
  Chirality :  0.036   0.143   2447
  Planarity :  0.005   0.076   1565
  Dihedral  : 30.323 150.403   4803
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.09 %
    Favored  : 84.48 %
  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:  2.25 (0.28), residues: 863
  helix:  2.25 (0.21), residues: 589
  sheet: -1.54 (1.35), residues: 12
  loop : -0.06 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP O 199 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.001   PHE O 254 
 TYR   0.014   0.001   TYR H  40 
 ARG   0.007   0.001   ARG G  99 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8769 (p) cc_final: 0.8267 (t)
REVERT: A   76 GLN cc_start: 0.8242 (mt0) cc_final: 0.7782 (mt0)
REVERT: C   13 LYS cc_start: 0.9144 (tppp) cc_final: 0.8849 (tppp)
REVERT: C   90 ASP cc_start: 0.8279 (t0) cc_final: 0.8028 (t0)
REVERT: C   91 GLU cc_start: 0.7758 (tp30) cc_final: 0.7537 (tp30)
REVERT: D   63 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8129 (m-40)
REVERT: D  108 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7803 (ptpp)
REVERT: D  119 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8036 (p)
REVERT: E   77 ASP cc_start: 0.8929 (m-30) cc_final: 0.8673 (t0)
REVERT: G   90 ASP cc_start: 0.8605 (t70) cc_final: 0.8306 (t0)
REVERT: G  104 GLN cc_start: 0.8717 (tp40) cc_final: 0.8517 (mm110)
REVERT: H   59 MET cc_start: 0.9147 (tpp) cc_final: 0.8819 (tpt)
REVERT: H  113 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8409 (tt0)
REVERT: O  190 MET cc_start: 0.6712 (ttp) cc_final: 0.6064 (tpp)
  outliers start: 18
  outliers final: 10
  residues processed: 136
  average time/residue: 1.7891
  time to fit residues: 259.5946
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   chunk 117 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
C  38 ASN
H  49 HIS
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.105849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069452 restraints weight = 35544.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.25
r_work: 0.3094 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15008  Z= 0.246
  Angle     :  0.605   9.810  21731  Z= 0.363
  Chirality :  0.035   0.127   2447
  Planarity :  0.005   0.077   1565
  Dihedral  : 30.388 149.364   4803
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.38 %
    Favored  : 82.73 %
  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:  2.35 (0.28), residues: 863
  helix:  2.29 (0.21), residues: 588
  sheet: -1.47 (1.35), residues: 12
  loop :  0.07 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP O 199 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.017   0.002   TYR O 197 
 ARG   0.006   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   90 ASP cc_start: 0.8275 (t0) cc_final: 0.8065 (t0)
REVERT: C   91 GLU cc_start: 0.7876 (tp30) cc_final: 0.7536 (tm-30)
REVERT: C   92 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8158 (mt-10)
REVERT: C   95 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8899 (ttmm)
REVERT: D   57 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8937 (mtpt)
REVERT: D   63 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8104 (m-40)
REVERT: D   71 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8225 (mt-10)
REVERT: D  108 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7780 (ptpp)
REVERT: E   63 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (mmm160)
REVERT: E   77 ASP cc_start: 0.8960 (m-30) cc_final: 0.8738 (t0)
REVERT: F   24 ASP cc_start: 0.8296 (t0) cc_final: 0.8071 (t0)
REVERT: G   90 ASP cc_start: 0.8474 (t70) cc_final: 0.8201 (t0)
REVERT: G  119 LYS cc_start: 0.8528 (mptt) cc_final: 0.8243 (mmtt)
REVERT: H   31 ARG cc_start: 0.8316 (pmt170) cc_final: 0.7779 (ptt90)
REVERT: H  113 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8435 (tt0)
REVERT: O  190 MET cc_start: 0.6686 (ttp) cc_final: 0.6245 (tpp)
  outliers start: 14
  outliers final: 7
  residues processed: 129
  average time/residue: 1.8456
  time to fit residues: 253.8177
Evaluate side-chains
  125 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 116 optimal weight:    0.0970
   chunk 88 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 113 HIS
C  38 ASN
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.105758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069563 restraints weight = 35449.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.30
r_work: 0.3117 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15008  Z= 0.242
  Angle     :  0.598   7.678  21731  Z= 0.359
  Chirality :  0.035   0.131   2447
  Planarity :  0.004   0.078   1565
  Dihedral  : 30.500 149.523   4803
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.25 %
    Favored  : 81.92 %
  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:  2.32 (0.28), residues: 863
  helix:  2.27 (0.21), residues: 590
  sheet: -1.21 (1.35), residues: 12
  loop :  0.01 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP O 214 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.018   0.002   TYR B  88 
 ARG   0.007   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8664 (p) cc_final: 0.8429 (p)
REVERT: C   90 ASP cc_start: 0.8290 (t0) cc_final: 0.8048 (t0)
REVERT: C   91 GLU cc_start: 0.7873 (tp30) cc_final: 0.7664 (tm-30)
REVERT: D   63 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8091 (m-40)
REVERT: D   71 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8279 (mt-10)
REVERT: D  108 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7908 (ptpp)
REVERT: E   77 ASP cc_start: 0.8964 (m-30) cc_final: 0.8729 (t0)
REVERT: F   24 ASP cc_start: 0.8262 (t0) cc_final: 0.8044 (t0)
REVERT: G   90 ASP cc_start: 0.8398 (t70) cc_final: 0.8103 (t0)
REVERT: G   95 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8640 (ttpp)
REVERT: G  116 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8802 (mt)
REVERT: H   31 ARG cc_start: 0.8384 (pmt170) cc_final: 0.7868 (ptt90)
REVERT: H   76 GLU cc_start: 0.9145 (tp30) cc_final: 0.8917 (mm-30)
REVERT: H  101 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (mm)
REVERT: H  113 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8447 (tt0)
  outliers start: 21
  outliers final: 8
  residues processed: 137
  average time/residue: 1.7947
  time to fit residues: 262.5454
Evaluate side-chains
  124 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 68 optimal weight:    0.5980
   chunk 105 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 110 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  38 ASN
** H  63 ASN ** 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 = 0.3926 r_free = 0.3926 target = 0.106159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.069951 restraints weight = 35901.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.29
r_work: 0.3103 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15008  Z= 0.231
  Angle     :  0.599   8.120  21731  Z= 0.357
  Chirality :  0.034   0.131   2447
  Planarity :  0.004   0.079   1565
  Dihedral  : 30.525 149.254   4803
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.20 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.87 %
    Favored  : 80.57 %
  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:  2.42 (0.28), residues: 863
  helix:  2.33 (0.21), residues: 590
  sheet: -1.02 (1.40), residues: 12
  loop :  0.08 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP O 199 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.022   0.002   TYR B  88 
 ARG   0.006   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8082 (mt-10)
REVERT: C   13 LYS cc_start: 0.9105 (tppp) cc_final: 0.8800 (tppp)
REVERT: C   90 ASP cc_start: 0.8287 (t0) cc_final: 0.8069 (t0)
REVERT: C   91 GLU cc_start: 0.7835 (tp30) cc_final: 0.7620 (tm-30)
REVERT: D   63 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8085 (m-40)
REVERT: D   71 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8262 (mt-10)
REVERT: D  108 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7837 (ptpp)
REVERT: E   77 ASP cc_start: 0.8946 (m-30) cc_final: 0.8720 (t0)
REVERT: F   24 ASP cc_start: 0.8214 (t0) cc_final: 0.7987 (t0)
REVERT: G   90 ASP cc_start: 0.8356 (t70) cc_final: 0.8100 (t0)
REVERT: G  116 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8799 (mt)
REVERT: G  119 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8414 (mmpt)
REVERT: H   31 ARG cc_start: 0.8187 (pmt170) cc_final: 0.7925 (ptt90)
REVERT: H  101 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: O  190 MET cc_start: 0.6714 (ttp) cc_final: 0.6300 (tpp)
  outliers start: 19
  outliers final: 9
  residues processed: 130
  average time/residue: 1.7649
  time to fit residues: 245.3039
Evaluate side-chains
  128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 117 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  38 ASN
G 104 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.106486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.070301 restraints weight = 35914.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.28
r_work: 0.3133 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15008  Z= 0.218
  Angle     :  0.588   7.160  21731  Z= 0.353
  Chirality :  0.034   0.132   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.506 149.069   4803
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.20 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.16 %
    Favored  : 79.08 %
  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:  2.45 (0.28), residues: 863
  helix:  2.35 (0.21), residues: 590
  sheet: -1.03 (1.43), residues: 12
  loop :  0.10 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP O 199 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.024   0.001   TYR B  88 
 ARG   0.007   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   13 LYS cc_start: 0.9137 (tppp) cc_final: 0.8811 (tppp)
REVERT: C   90 ASP cc_start: 0.8229 (t0) cc_final: 0.8026 (t0)
REVERT: D   63 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8067 (m-40)
REVERT: D  108 LYS cc_start: 0.8106 (ptmm) cc_final: 0.7822 (ptpp)
REVERT: E   77 ASP cc_start: 0.8949 (m-30) cc_final: 0.8726 (t0)
REVERT: G   90 ASP cc_start: 0.8326 (t70) cc_final: 0.8045 (t0)
REVERT: G  116 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8805 (mt)
REVERT: H  101 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8675 (mm)
REVERT: O  190 MET cc_start: 0.6716 (ttp) cc_final: 0.6349 (tpp)
  outliers start: 13
  outliers final: 7
  residues processed: 128
  average time/residue: 1.8744
  time to fit residues: 256.3439
Evaluate side-chains
  128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 117 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.105990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069519 restraints weight = 35805.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.30
r_work: 0.3098 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15008  Z= 0.250
  Angle     :  0.612  10.106  21731  Z= 0.362
  Chirality :  0.035   0.133   2447
  Planarity :  0.005   0.080   1565
  Dihedral  : 30.587 149.582   4803
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.62 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.36 (0.28), residues: 863
  helix:  2.28 (0.21), residues: 590
  sheet: -1.22 (1.39), residues: 12
  loop :  0.08 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP O 199 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.028   0.002   TYR B  88 
 ARG   0.007   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8106 (mt-10)
REVERT: C   13 LYS cc_start: 0.9156 (tppp) cc_final: 0.8819 (tppp)
REVERT: C   50 TYR cc_start: 0.8981 (t80) cc_final: 0.8776 (t80)
REVERT: C   64 GLU cc_start: 0.7833 (tp30) cc_final: 0.7554 (mm-30)
REVERT: C   90 ASP cc_start: 0.8268 (t0) cc_final: 0.8015 (t0)
REVERT: D   63 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8117 (m-40)
REVERT: D  108 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7850 (ptpp)
REVERT: E   77 ASP cc_start: 0.8957 (m-30) cc_final: 0.8725 (t0)
REVERT: F   24 ASP cc_start: 0.8154 (t0) cc_final: 0.7949 (t0)
REVERT: G   90 ASP cc_start: 0.8375 (t70) cc_final: 0.8094 (t0)
REVERT: G  116 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8776 (mt)
REVERT: H   31 ARG cc_start: 0.8224 (pmt170) cc_final: 0.7730 (ttp-170)
REVERT: H  101 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8700 (mm)
REVERT: H  113 GLU cc_start: 0.8528 (tt0) cc_final: 0.8168 (tm-30)
REVERT: O  190 MET cc_start: 0.6790 (ttp) cc_final: 0.6361 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 127
  average time/residue: 1.8194
  time to fit residues: 246.9486
Evaluate side-chains
  129 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.106842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.070763 restraints weight = 35696.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.27
r_work: 0.3122 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15008  Z= 0.196
  Angle     :  0.596   9.193  21731  Z= 0.355
  Chirality :  0.034   0.137   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.536 149.054   4803
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.85 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.70 %
    Favored  : 78.41 %
  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:  2.46 (0.28), residues: 863
  helix:  2.34 (0.21), residues: 590
  sheet: -1.26 (1.38), residues: 12
  loop :  0.15 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP O 199 
 HIS   0.002   0.000   HIS F  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.034   0.002   TYR B  88 
 ARG   0.008   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   13 LYS cc_start: 0.9185 (tppp) cc_final: 0.8854 (tppp)
REVERT: C   50 TYR cc_start: 0.8947 (t80) cc_final: 0.8692 (t80)
REVERT: C   91 GLU cc_start: 0.7774 (tp30) cc_final: 0.7495 (tm-30)
REVERT: D   63 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8039 (m-40)
REVERT: D  108 LYS cc_start: 0.8037 (ptmm) cc_final: 0.7723 (ptpp)
REVERT: E   77 ASP cc_start: 0.8948 (m-30) cc_final: 0.8724 (t0)
REVERT: G   90 ASP cc_start: 0.8359 (t70) cc_final: 0.8049 (t0)
REVERT: G  116 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (mt)
REVERT: H   31 ARG cc_start: 0.8197 (pmt170) cc_final: 0.7714 (ttp-170)
REVERT: H   40 TYR cc_start: 0.8674 (m-80) cc_final: 0.8298 (m-80)
REVERT: H  101 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8688 (mm)
REVERT: H  113 GLU cc_start: 0.8409 (tt0) cc_final: 0.8050 (tm-30)
REVERT: O  190 MET cc_start: 0.6734 (ttp) cc_final: 0.6241 (tpp)
REVERT: O  215 GLN cc_start: 0.7183 (pp30) cc_final: 0.6977 (pp30)
  outliers start: 14
  outliers final: 7
  residues processed: 133
  average time/residue: 1.7874
  time to fit residues: 253.8371
Evaluate side-chains
  127 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 168 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.106589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.070758 restraints weight = 35553.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.21
r_work: 0.3122 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15008  Z= 0.224
  Angle     :  0.623  11.961  21731  Z= 0.364
  Chirality :  0.034   0.153   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.503 149.147   4803
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.51 %
    Favored  : 77.60 %
  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:  2.43 (0.28), residues: 863
  helix:  2.31 (0.21), residues: 590
  sheet: -1.07 (1.40), residues: 12
  loop :  0.15 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP O 214 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.038   0.002   TYR B  88 
 ARG   0.008   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8679 (p) cc_final: 0.7999 (t)
REVERT: C   13 LYS cc_start: 0.9197 (tppp) cc_final: 0.8857 (tppp)
REVERT: D   63 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8067 (m-40)
REVERT: D  108 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7781 (ptpp)
REVERT: E   77 ASP cc_start: 0.8935 (m-30) cc_final: 0.8718 (t0)
REVERT: F   24 ASP cc_start: 0.8274 (t0) cc_final: 0.8062 (t0)
REVERT: G   90 ASP cc_start: 0.8382 (t70) cc_final: 0.8099 (t0)
REVERT: G  116 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8634 (mt)
REVERT: H   31 ARG cc_start: 0.8183 (pmt170) cc_final: 0.7726 (ttp-170)
REVERT: H  101 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8696 (mm)
REVERT: H  113 GLU cc_start: 0.8537 (tt0) cc_final: 0.8141 (tm-30)
REVERT: O  215 GLN cc_start: 0.6970 (pp30) cc_final: 0.6767 (pp30)
REVERT: O  253 MET cc_start: 0.5615 (tpt) cc_final: 0.1844 (mtt)
  outliers start: 14
  outliers final: 10
  residues processed: 130
  average time/residue: 1.8043
  time to fit residues: 251.5834
Evaluate side-chains
  131 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 114 optimal weight:    0.3980
   chunk 103 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0670
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.107569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071718 restraints weight = 35560.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.26
r_work: 0.3145 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  15008  Z= 0.200
  Angle     :  0.615  10.904  21731  Z= 0.361
  Chirality :  0.034   0.254   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.405 148.587   4803
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.85 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 21.05 %
    Favored  : 77.46 %
  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:  2.49 (0.28), residues: 863
  helix:  2.37 (0.21), residues: 590
  sheet: -1.39 (1.36), residues: 12
  loop :  0.18 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP O 199 
 HIS   0.002   0.001   HIS H  49 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.042   0.002   TYR B  88 
 ARG   0.008   0.000   ARG H  86 

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

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

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1726 Ramachandran restraints generated.
    863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8602 (p) cc_final: 0.7933 (t)
REVERT: C   13 LYS cc_start: 0.9246 (tppp) cc_final: 0.8924 (tppp)
REVERT: D   63 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8039 (m-40)
REVERT: D  108 LYS cc_start: 0.8076 (ptmm) cc_final: 0.7743 (ptpp)
REVERT: E   77 ASP cc_start: 0.8939 (m-30) cc_final: 0.8732 (t0)
REVERT: F   24 ASP cc_start: 0.8299 (t0) cc_final: 0.7992 (t0)
REVERT: G   90 ASP cc_start: 0.8360 (t70) cc_final: 0.8036 (t0)
REVERT: H   31 ARG cc_start: 0.8225 (pmt170) cc_final: 0.7712 (ttp-170)
REVERT: H  101 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8676 (mm)
REVERT: H  113 GLU cc_start: 0.8532 (tt0) cc_final: 0.8104 (tm-30)
REVERT: O  215 GLN cc_start: 0.6972 (pp30) cc_final: 0.6759 (pp30)
REVERT: O  253 MET cc_start: 0.5467 (tpt) cc_final: 0.1759 (mtt)
  outliers start: 11
  outliers final: 7
  residues processed: 124
  average time/residue: 1.8731
  time to fit residues: 247.5376
Evaluate side-chains
  121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   63 ASN
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain O residue  220 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 117 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.106898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.071065 restraints weight = 35972.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.06
r_work: 0.3151 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  15008  Z= 0.222
  Angle     :  0.634  12.255  21731  Z= 0.367
  Chirality :  0.035   0.205   2447
  Planarity :  0.004   0.080   1565
  Dihedral  : 30.428 148.940   4803
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.09 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 22.13 %
    Favored  : 76.65 %
  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:  2.45 (0.28), residues: 863
  helix:  2.35 (0.21), residues: 590
  sheet: -1.22 (1.39), residues: 12
  loop :  0.11 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP O 199 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.043   0.002   TYR B  88 
 ARG   0.008   0.000   ARG H  86 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11346.46 seconds
wall clock time: 201 minutes 1.84 seconds (12061.84 seconds total)