Starting phenix.real_space_refine
on Sat Sep 12 00:03:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktq_23026/09_2026/7ktq_23026.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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     331      5.49       5
     S      12      5.16       5
     C    6973      2.51       5
     N    2384      2.21       5
     O    3045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12745
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3343
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3441
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 2.67, per 1000 atoms: 0.21
  Number of scatterers: 12745
  At special positions: 0
  Unit cell: (76.95, 121.5, 147.15, 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      12     16.00
     P     331     15.00
     O    3045      8.00
     N    2384      7.00
     C    6973      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: 0.80
  Conformation dependent library (CDL) restraints added in 337.9 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      71.0% alpha, 3.2% beta
      117 base pairs and 288 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.709A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.884A  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 131
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.551A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 3.652A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.710A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.651A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.552A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 3.674A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.715A  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 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  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: 6.310A  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: 7.173A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.964A  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: 7.192A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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

    400 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      300 hydrogen bonds
      596 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      288 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 1.18 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: 2203
        1.33 -     1.45: 4715
        1.45 -     1.57: 6049
        1.57 -     1.69: 661
        1.69 -     1.80: 22
  Bond restraints: 13650
  Sorted by residual:
  bond pdb=" C3'  DA J  83 "
       pdb=" C2'  DA J  83 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.68e+01
  bond pdb=" C3'  DT J 106 "
       pdb=" O3'  DT J 106 "
    ideal  model  delta    sigma   weight residual
    1.435  1.487 -0.052 1.30e-02 5.92e+03 1.57e+01
  bond pdb=" C3'  DA J  72 "
       pdb=" O3'  DA J  72 "
    ideal  model  delta    sigma   weight residual
    1.435  1.386  0.049 1.30e-02 5.92e+03 1.43e+01
  bond pdb=" C3'  DT J  17 "
       pdb=" O3'  DT J  17 "
    ideal  model  delta    sigma   weight residual
    1.435  1.388  0.047 1.30e-02 5.92e+03 1.29e+01
  bond pdb=" C3'  DG J 102 "
       pdb=" O3'  DG J 102 "
    ideal  model  delta    sigma   weight residual
    1.435  1.388  0.047 1.30e-02 5.92e+03 1.29e+01
  ... (remaining 13645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 17850
        1.65 -     3.29: 1832
        3.29 -     4.94: 157
        4.94 -     6.58: 22
        6.58 -     8.23: 4
  Bond angle restraints: 19865
  Sorted by residual:
  angle pdb=" O5'  DG J  14 "
        pdb=" C5'  DG J  14 "
        pdb=" C4'  DG J  14 "
      ideal   model   delta    sigma   weight residual
     109.40  115.24   -5.84 8.00e-01 1.56e+00 5.32e+01
  angle pdb=" O5'  DT I 146 "
        pdb=" C5'  DT I 146 "
        pdb=" C4'  DT I 146 "
      ideal   model   delta    sigma   weight residual
     109.40  114.69   -5.29 8.00e-01 1.56e+00 4.38e+01
  angle pdb=" O5'  DC I  64 "
        pdb=" C5'  DC I  64 "
        pdb=" C4'  DC I  64 "
      ideal   model   delta    sigma   weight residual
     109.40  114.36   -4.96 8.00e-01 1.56e+00 3.84e+01
  angle pdb=" O5'  DG I  77 "
        pdb=" C5'  DG I  77 "
        pdb=" C4'  DG I  77 "
      ideal   model   delta    sigma   weight residual
     109.40  113.51   -4.11 8.00e-01 1.56e+00 2.65e+01
  angle pdb=" O4'  DT I  58 "
        pdb=" C4'  DT I  58 "
        pdb=" C3'  DT I  58 "
      ideal   model   delta    sigma   weight residual
     106.00  102.94    3.06 6.00e-01 2.78e+00 2.61e+01
  ... (remaining 19860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 5693
       35.95 -    71.89: 1623
       71.89 -   107.84: 21
      107.84 -   143.79: 0
      143.79 -   179.74: 5
  Dihedral angle restraints: 7342
    sinusoidal: 5160
      harmonic: 2182
  Sorted by residual:
  dihedral pdb=" C4'  DC I   3 "
           pdb=" C3'  DC I   3 "
           pdb=" O3'  DC I   3 "
           pdb=" P    DC I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.74 -179.74     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I 104 "
           pdb=" C3'  DG I 104 "
           pdb=" O3'  DG I 104 "
           pdb=" P    DC I 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.45  179.55     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J 106 "
           pdb=" C3'  DT J 106 "
           pdb=" O3'  DT J 106 "
           pdb=" P    DG J 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.30  177.70     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1597
       0.059 -    0.118: 567
       0.118 -    0.177: 91
       0.177 -    0.236: 5
       0.236 -    0.295: 2
  Chirality restraints: 2262
  Sorted by residual:
  chirality pdb=" CG  LEU G 115 "
            pdb=" CB  LEU G 115 "
            pdb=" CD1 LEU G 115 "
            pdb=" CD2 LEU G 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" C1'  DG J  66 "
            pdb=" O4'  DG J  66 "
            pdb=" C2'  DG J  66 "
            pdb=" N9   DG J  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.18    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" C3'  DG I 104 "
            pdb=" C4'  DG I 104 "
            pdb=" O3'  DG I 104 "
            pdb=" C2'  DG I 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.50   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 2259 not shown)

  Planarity restraints: 1368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 106 "    0.005 2.00e-02 2.50e+03   3.37e-02 2.55e+01
        pdb=" N1   DC I 106 "   -0.025 2.00e-02 2.50e+03
        pdb=" C2   DC I 106 "    0.083 2.00e-02 2.50e+03
        pdb=" O2   DC I 106 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3   DC I 106 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DC I 106 "    0.016 2.00e-02 2.50e+03
        pdb=" N4   DC I 106 "   -0.014 2.00e-02 2.50e+03
        pdb=" C5   DC I 106 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC I 106 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  87 "   -0.043 2.00e-02 2.50e+03   2.87e-02 1.86e+01
        pdb=" N1   DC J  87 "    0.068 2.00e-02 2.50e+03
        pdb=" C2   DC J  87 "   -0.027 2.00e-02 2.50e+03
        pdb=" O2   DC J  87 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DC J  87 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DC J  87 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  87 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DC J  87 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J  87 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS H 106 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   HIS H 106 "    0.073 2.00e-02 2.50e+03
        pdb=" O   HIS H 106 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ALA H 107 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1365 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1483
        2.74 -     3.28: 10850
        3.28 -     3.82: 24023
        3.82 -     4.36: 29764
        4.36 -     4.90: 41980
  Nonbonded interactions: 108100
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B  74 "
            pdb=" NH2 ARG D  96 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" C2'  DA J  20 "
            pdb=" C7   DT J  21 "
     model   vdw
     2.274 3.860
  nonbonded pdb=" OE1 GLU F  74 "
            pdb=" NH2 ARG H  96 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O6   DG I  44 "
            pdb=" N4   DC J 124 "
     model   vdw
     2.313 3.120
  ... (remaining 108095 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 117)
  selection = chain 'G'
}
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:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.120
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
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      :  0.008   0.067  13650  Z= 0.676
  Angle     :  0.985   8.228  19865  Z= 0.820
  Chirality :  0.058   0.295   2262
  Planarity :  0.009   0.043   1368
  Dihedral  : 29.268 179.736   5934
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.24), residues: 736
  helix: -1.35 (0.18), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.86 (0.34), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  83 
 TYR   0.015   0.002   TYR F  98 
 PHE   0.016   0.003   PHE C  25 
 HIS   0.012   0.002   HIS H  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00850 /  0.68 (13650)
  covalent geometry    : angle       0.98516 /  0.82 (19865)
  hydrogen bonds       : bond        0.14041 /  9.31 (  700)
  hydrogen bonds       : angle       6.28309 /  4.44 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7634 (mt-10)
REVERT: D   30 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7046 (ptm160)
REVERT: D   65 ASP cc_start: 0.8839 (t0) cc_final: 0.8598 (t0)
REVERT: D  113 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8092 (tttp)
REVERT: D  116 THR cc_start: 0.8694 (m) cc_final: 0.8245 (p)
REVERT: D  117 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8657 (ttmt)
REVERT: E   90 MET cc_start: 0.8070 (tpp) cc_final: 0.7567 (mmm)
REVERT: F   35 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7852 (mtm110)
REVERT: G   36 LYS cc_start: 0.8465 (pttp) cc_final: 0.7836 (mmmt)
REVERT: G   75 LYS cc_start: 0.8463 (mttt) cc_final: 0.8194 (mtpt)
REVERT: G   95 LYS cc_start: 0.8683 (tptt) cc_final: 0.8434 (tptt)
REVERT: H   40 LYS cc_start: 0.8557 (mttm) cc_final: 0.8255 (mttt)
REVERT: H   64 ASN cc_start: 0.9031 (m-40) cc_final: 0.8809 (m-40)
REVERT: H  117 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8436 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1986
  time to fit residues: 47.4041
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
B  93 GLN
D  81 ASN
F  27 GLN
G  38 ASN
G  73 ASN
G 110 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.157225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108135 restraints weight = 17666.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 0.93
r_work: 0.3063 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  13650  Z= 0.155
  Angle     :  0.655   7.002  19865  Z= 0.380
  Chirality :  0.048   0.283   2262
  Planarity :  0.005   0.043   1368
  Dihedral  : 32.891 179.293   4452
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.44 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.29), residues: 736
  helix:  1.24 (0.21), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.23 (0.37), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  76 
 TYR   0.010   0.001   TYR F  98 
 PHE   0.010   0.001   PHE C  25 
 HIS   0.004   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.15 (13650)
  covalent geometry    : angle       0.65536 /  0.38 (19865)
  hydrogen bonds       : bond        0.06533 /  4.25 (  700)
  hydrogen bonds       : angle       3.28758 /  2.37 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 140
  time to evaluate  : 0.329 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.8931 (ttm170) cc_final: 0.8722 (ttm170)
REVERT: D   30 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6926 (ptm160)
REVERT: D   80 TYR cc_start: 0.8600 (m-10) cc_final: 0.7688 (m-10)
REVERT: D  113 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8395 (tttp)
REVERT: D  116 THR cc_start: 0.8857 (m) cc_final: 0.8335 (p)
REVERT: D  117 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8743 (ttmt)
REVERT: E   90 MET cc_start: 0.8776 (tpp) cc_final: 0.8430 (mmm)
REVERT: F   35 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8319 (mtm110)
REVERT: F   68 ASP cc_start: 0.9290 (m-30) cc_final: 0.9010 (m-30)
REVERT: G   35 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7925 (mtm110)
REVERT: G   36 LYS cc_start: 0.8639 (pttp) cc_final: 0.8089 (mmmt)
REVERT: G   75 LYS cc_start: 0.8551 (mttt) cc_final: 0.8250 (mtpt)
REVERT: G   95 LYS cc_start: 0.9045 (tptt) cc_final: 0.8756 (tptt)
REVERT: H   40 LYS cc_start: 0.8745 (mttm) cc_final: 0.8509 (mttt)
  outliers start: 6
  outliers final: 3
  residues processed: 142
  average time/residue: 0.1446
  time to fit residues: 27.9357
Evaluate side-chains
  128 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.155406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.105726 restraints weight = 17895.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 0.94
r_work: 0.3029 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13650  Z= 0.169
  Angle     :  0.620   6.245  19865  Z= 0.357
  Chirality :  0.045   0.310   2262
  Planarity :  0.005   0.040   1368
  Dihedral  : 32.700 179.541   4452
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.40 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.30), residues: 736
  helix:  2.20 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.91 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  69 
 TYR   0.013   0.002   TYR D  37 
 PHE   0.014   0.002   PHE C  25 
 HIS   0.005   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 (13650)
  covalent geometry    : angle       0.62034 /  0.36 (19865)
  hydrogen bonds       : bond        0.05862 /  3.94 (  700)
  hydrogen bonds       : angle       3.06551 /  2.23 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.312 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.8991 (ttm170) cc_final: 0.8777 (ttm170)
REVERT: D   30 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7013 (ptm160)
REVERT: D   80 TYR cc_start: 0.8686 (m-10) cc_final: 0.7919 (m-10)
REVERT: D  113 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8523 (tttp)
REVERT: D  116 THR cc_start: 0.8956 (m) cc_final: 0.8354 (p)
REVERT: E   90 MET cc_start: 0.8752 (tpp) cc_final: 0.8527 (mmm)
REVERT: F   35 ARG cc_start: 0.8758 (mmm160) cc_final: 0.8449 (mtm110)
REVERT: F   68 ASP cc_start: 0.9291 (m-30) cc_final: 0.8997 (m-30)
REVERT: G   35 ARG cc_start: 0.8187 (mtp-110) cc_final: 0.7939 (mtm110)
REVERT: G   36 LYS cc_start: 0.8568 (pttp) cc_final: 0.8135 (mmmt)
REVERT: G   95 LYS cc_start: 0.8985 (tptt) cc_final: 0.8732 (tptt)
REVERT: G  110 ASN cc_start: 0.8542 (t0) cc_final: 0.8232 (t0)
REVERT: H   39 TYR cc_start: 0.8453 (t80) cc_final: 0.7638 (t80)
REVERT: H   40 LYS cc_start: 0.8757 (mttm) cc_final: 0.8539 (mttt)
REVERT: H   99 LEU cc_start: 0.9417 (mt) cc_final: 0.9212 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1417
  time to fit residues: 25.0353
Evaluate side-chains
  124 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:   10.0000
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
C  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.156278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.106903 restraints weight = 17752.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 0.93
r_work: 0.3013 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13650  Z= 0.137
  Angle     :  0.570   6.107  19865  Z= 0.336
  Chirality :  0.042   0.310   2262
  Planarity :  0.004   0.040   1368
  Dihedral  : 32.414 179.195   4452
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.20 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.30), residues: 736
  helix:  2.64 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.84 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.007   0.001   PHE C  25 
 HIS   0.003   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.14 (13650)
  covalent geometry    : angle       0.57027 /  0.34 (19865)
  hydrogen bonds       : bond        0.05143 /  3.41 (  700)
  hydrogen bonds       : angle       2.89343 /  2.10 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.335 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8790 (ttm170)
REVERT: D   30 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6815 (ptp-170)
REVERT: D   80 TYR cc_start: 0.8617 (m-10) cc_final: 0.7677 (m-10)
REVERT: D  113 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8612 (tttp)
REVERT: D  116 THR cc_start: 0.8936 (m) cc_final: 0.8333 (p)
REVERT: E   90 MET cc_start: 0.8731 (tpp) cc_final: 0.8516 (mmm)
REVERT: E  122 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8167 (mtmt)
REVERT: F   35 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8452 (mtm110)
REVERT: F   68 ASP cc_start: 0.9289 (m-30) cc_final: 0.8960 (m-30)
REVERT: G   35 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7975 (mtm110)
REVERT: G   36 LYS cc_start: 0.8574 (pttp) cc_final: 0.8129 (mmmt)
REVERT: G   95 LYS cc_start: 0.9001 (tptt) cc_final: 0.8784 (tptt)
REVERT: G  110 ASN cc_start: 0.8570 (t0) cc_final: 0.8266 (t0)
REVERT: H   39 TYR cc_start: 0.8469 (t80) cc_final: 0.7689 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 128
  average time/residue: 0.1500
  time to fit residues: 25.9050
Evaluate side-chains
  126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 88 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
C  84 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.155162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.105632 restraints weight = 17826.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 0.93
r_work: 0.3024 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  13650  Z= 0.148
  Angle     :  0.579   6.454  19865  Z= 0.337
  Chirality :  0.043   0.312   2262
  Planarity :  0.004   0.039   1368
  Dihedral  : 32.263 179.507   4452
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.36 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.31), residues: 736
  helix:  2.77 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.85 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  69 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.009   0.002   PHE C  25 
 HIS   0.003   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.15 (13650)
  covalent geometry    : angle       0.57932 /  0.34 (19865)
  hydrogen bonds       : bond        0.05350 /  3.60 (  700)
  hydrogen bonds       : angle       2.89966 /  2.12 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8761 (pm20) cc_final: 0.8554 (pm20)
REVERT: B   26 ILE cc_start: 0.9114 (tp) cc_final: 0.8872 (tp)
REVERT: C   20 ARG cc_start: 0.9047 (ttm170) cc_final: 0.8834 (ttm170)
REVERT: D   30 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6955 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8663 (tttp)
REVERT: D  116 THR cc_start: 0.8951 (m) cc_final: 0.8365 (p)
REVERT: E   90 MET cc_start: 0.8738 (tpp) cc_final: 0.8531 (mmm)
REVERT: E  122 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8153 (mtmt)
REVERT: F   35 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8456 (mtm110)
REVERT: G   35 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7996 (mtm110)
REVERT: G   36 LYS cc_start: 0.8604 (pttp) cc_final: 0.8217 (mmmt)
REVERT: G   95 LYS cc_start: 0.9001 (tptt) cc_final: 0.8789 (tptt)
REVERT: H   31 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8233 (ttpt)
REVERT: H   39 TYR cc_start: 0.8575 (t80) cc_final: 0.7739 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 132
  average time/residue: 0.1484
  time to fit residues: 26.6110
Evaluate side-chains
  127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 122
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.4823 > 50:)
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
** D  92 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 = 0.3817 r_free = 0.3817 target = 0.151039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.099976 restraints weight = 17842.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.15
r_work: 0.2900 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13650  Z= 0.220
  Angle     :  0.662   8.101  19865  Z= 0.369
  Chirality :  0.048   0.315   2262
  Planarity :  0.005   0.041   1368
  Dihedral  : 32.332 178.893   4452
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.00 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.30), residues: 736
  helix:  2.46 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.08 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  83 
 TYR   0.015   0.002   TYR F  51 
 PHE   0.014   0.002   PHE F 100 
 HIS   0.007   0.002   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00470 /  0.22 (13650)
  covalent geometry    : angle       0.66183 /  0.37 (19865)
  hydrogen bonds       : bond        0.06182 /  4.17 (  700)
  hydrogen bonds       : angle       3.09798 /  2.25 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.314 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.9023 (ttm170) cc_final: 0.8794 (ttm170)
REVERT: D   30 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6910 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8666 (tttp)
REVERT: E   90 MET cc_start: 0.8978 (tpp) cc_final: 0.8719 (mmm)
REVERT: E  122 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8345 (mtmt)
REVERT: E  129 ARG cc_start: 0.8437 (tpt90) cc_final: 0.8121 (tpt90)
REVERT: F   35 ARG cc_start: 0.8894 (mmm160) cc_final: 0.8437 (mtm110)
REVERT: G   35 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7977 (mtm110)
REVERT: G   36 LYS cc_start: 0.8678 (pttp) cc_final: 0.8191 (mmmt)
  outliers start: 10
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1553
  time to fit residues: 26.0928
Evaluate side-chains
  125 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  115 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 73 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
D  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.152312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.101497 restraints weight = 17744.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.17
r_work: 0.2924 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13650  Z= 0.138
  Angle     :  0.613   7.392  19865  Z= 0.350
  Chirality :  0.045   0.309   2262
  Planarity :  0.004   0.036   1368
  Dihedral  : 32.277 179.470   4452
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.96 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.31), residues: 736
  helix:  2.69 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.014   0.001   TYR F  51 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.005   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.14 (13650)
  covalent geometry    : angle       0.61282 /  0.35 (19865)
  hydrogen bonds       : bond        0.05629 /  3.78 (  700)
  hydrogen bonds       : angle       3.02404 /  2.20 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.311 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8770 (ttm170)
REVERT: D   30 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6918 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8642 (tttp)
REVERT: E   90 MET cc_start: 0.8956 (tpp) cc_final: 0.8696 (mmm)
REVERT: E  122 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8288 (mtmt)
REVERT: E  129 ARG cc_start: 0.8503 (tpt90) cc_final: 0.8172 (tpt90)
REVERT: F   35 ARG cc_start: 0.8880 (mmm160) cc_final: 0.8446 (mtm110)
REVERT: G   35 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7922 (mtm110)
REVERT: G   36 LYS cc_start: 0.8652 (pttp) cc_final: 0.8164 (mmmt)
  outliers start: 9
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1563
  time to fit residues: 26.5779
Evaluate side-chains
  129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 6 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0470
   chunk 45 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.5878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
D  46 HIS
F  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.152680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.102112 restraints weight = 17687.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.16
r_work: 0.2917 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13650  Z= 0.145
  Angle     :  0.597   7.052  19865  Z= 0.343
  Chirality :  0.044   0.315   2262
  Planarity :  0.004   0.035   1368
  Dihedral  : 32.201 179.843   4452
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.44 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.31), residues: 736
  helix:  2.77 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.95 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 129 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.007   0.001   PHE D  62 
 HIS   0.004   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 (13650)
  covalent geometry    : angle       0.59745 /  0.34 (19865)
  hydrogen bonds       : bond        0.05427 /  3.65 (  700)
  hydrogen bonds       : angle       2.94412 /  2.15 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9052 (m-10) cc_final: 0.8469 (m-80)
REVERT: C   20 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8768 (ttm170)
REVERT: D   30 ARG cc_start: 0.7894 (mtt180) cc_final: 0.6945 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8672 (tttp)
REVERT: E   90 MET cc_start: 0.8911 (tpp) cc_final: 0.8653 (mmm)
REVERT: E  122 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8288 (mtmt)
REVERT: E  129 ARG cc_start: 0.8493 (tpt90) cc_final: 0.8171 (tpt90)
REVERT: F   35 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8426 (mtm110)
REVERT: G   35 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7921 (mtm110)
REVERT: G   36 LYS cc_start: 0.8647 (pttp) cc_final: 0.8200 (mmmt)
REVERT: G   38 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8389 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 128
  average time/residue: 0.1580
  time to fit residues: 26.9368
Evaluate side-chains
  126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 86 optimal weight:   30.0000
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.152949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.102534 restraints weight = 17768.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.15
r_work: 0.2946 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13650  Z= 0.145
  Angle     :  0.586   6.882  19865  Z= 0.339
  Chirality :  0.043   0.310   2262
  Planarity :  0.004   0.035   1368
  Dihedral  : 32.154 179.880   4452
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.76 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.31), residues: 736
  helix:  2.82 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.91 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  83 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.006   0.001   PHE C  25 
 HIS   0.004   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.14 (13650)
  covalent geometry    : angle       0.58577 /  0.34 (19865)
  hydrogen bonds       : bond        0.05347 /  3.59 (  700)
  hydrogen bonds       : angle       2.92714 /  2.13 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8801 (pm20) cc_final: 0.8410 (pm20)
REVERT: B   88 TYR cc_start: 0.9073 (m-10) cc_final: 0.8476 (m-80)
REVERT: C   20 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8818 (ttm170)
REVERT: D   30 ARG cc_start: 0.7905 (mtt180) cc_final: 0.6942 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8667 (tttp)
REVERT: E   90 MET cc_start: 0.8901 (tpp) cc_final: 0.8652 (mmm)
REVERT: E  122 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8297 (mtmt)
REVERT: E  129 ARG cc_start: 0.8495 (tpt90) cc_final: 0.8172 (tpt90)
REVERT: F   35 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8443 (mtm110)
REVERT: G   35 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7931 (mtm110)
REVERT: G   36 LYS cc_start: 0.8644 (pttp) cc_final: 0.8199 (mmmt)
REVERT: G   38 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8404 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 128
  average time/residue: 0.1654
  time to fit residues: 28.2723
Evaluate side-chains
  130 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 92 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0010
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.153025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.102512 restraints weight = 17793.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.15
r_work: 0.2942 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13650  Z= 0.136
  Angle     :  0.580   6.803  19865  Z= 0.336
  Chirality :  0.043   0.312   2262
  Planarity :  0.004   0.035   1368
  Dihedral  : 32.135 179.893   4452
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 13.60 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.92 (0.31), residues: 736
  helix:  2.85 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.88 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  83 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.007   0.001   PHE D  62 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.14 (13650)
  covalent geometry    : angle       0.57998 /  0.34 (19865)
  hydrogen bonds       : bond        0.05272 /  3.54 (  700)
  hydrogen bonds       : angle       2.90523 /  2.12 ( 1796)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.310 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9064 (m-10) cc_final: 0.8470 (m-80)
REVERT: C   20 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8819 (ttm170)
REVERT: D   30 ARG cc_start: 0.7896 (mtt180) cc_final: 0.6946 (ptp-170)
REVERT: D  113 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8667 (tttp)
REVERT: E   90 MET cc_start: 0.8857 (tpp) cc_final: 0.8595 (mmm)
REVERT: E  122 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8275 (mtmt)
REVERT: E  129 ARG cc_start: 0.8496 (tpt90) cc_final: 0.8173 (tpt90)
REVERT: F   35 ARG cc_start: 0.8857 (mmm160) cc_final: 0.8449 (mtm110)
REVERT: G   35 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7917 (mtm110)
REVERT: G   36 LYS cc_start: 0.8644 (pttp) cc_final: 0.8196 (mmmt)
REVERT: G   38 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8407 (m110)
  outliers start: 7
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1581
  time to fit residues: 27.2008
Evaluate side-chains
  131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 89 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 86 optimal weight:   30.0000
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
F  93 GLN
G  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.152577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.102029 restraints weight = 17680.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.14
r_work: 0.2931 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13650  Z= 0.160
  Angle     :  0.588   7.109  19865  Z= 0.339
  Chirality :  0.044   0.317   2262
  Planarity :  0.004   0.036   1368
  Dihedral  : 32.055 179.083   4452
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 13.60 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.31), residues: 736
  helix:  2.79 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.88 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.016   0.001   TYR F  51 
 PHE   0.011   0.002   PHE A  78 
 HIS   0.004   0.001   HIS D  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.16 (13650)
  covalent geometry    : angle       0.58793 /  0.34 (19865)
  hydrogen bonds       : bond        0.05359 /  3.62 (  700)
  hydrogen bonds       : angle       2.90468 /  2.12 ( 1796)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3262.80 seconds
wall clock time: 56 minutes 22.11 seconds (3382.11 seconds total)