Starting phenix.real_space_refine
on Wed Mar  4 09:11:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktq_23026/03_2026/7ktq_23026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktq_23026/03_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_23026/03_2026/7ktq_23026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktq_23026/03_2026/7ktq_23026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktq_23026/03_2026/7ktq_23026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktq_23026/03_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-dev-5986/lib/python3.9/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: 2.70, 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: 0.92
  Conformation dependent library (CDL) restraints added in 374.3 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: 1.87
  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: 2.29

  Time building geometry restraints manager: 1.32 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=" O5'  DA J  83 "
       pdb=" C5'  DA J  83 "
    ideal  model  delta    sigma   weight residual
    1.423  1.351  0.072 3.00e-02 1.11e+03 5.72e+00
  bond pdb=" C3'  DT J 106 "
       pdb=" O3'  DT J 106 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.62e+00
  bond pdb=" O5'  DC I  64 "
       pdb=" C5'  DC I  64 "
    ideal  model  delta    sigma   weight residual
    1.423  1.360  0.063 3.00e-02 1.11e+03 4.41e+00
  bond pdb=" O5'  DG J 102 "
       pdb=" C5'  DG J 102 "
    ideal  model  delta    sigma   weight residual
    1.423  1.363  0.060 3.00e-02 1.11e+03 3.99e+00
  bond pdb=" O5'  DT J  17 "
       pdb=" C5'  DT J  17 "
    ideal  model  delta    sigma   weight residual
    1.423  1.366  0.057 3.00e-02 1.11e+03 3.56e+00
  ... (remaining 13645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 18537
        1.65 -     3.29: 1229
        3.29 -     4.94: 79
        4.94 -     6.58: 16
        6.58 -     8.23: 4
  Bond angle restraints: 19865
  Sorted by residual:
  angle pdb=" C   ARG E  40 "
        pdb=" N   TYR E  41 "
        pdb=" CA  TYR E  41 "
      ideal   model   delta    sigma   weight residual
     122.03  113.80    8.23 2.01e+00 2.48e-01 1.68e+01
  angle pdb=" N   ILE F  26 "
        pdb=" CA  ILE F  26 "
        pdb=" C   ILE F  26 "
      ideal   model   delta    sigma   weight residual
     112.50  107.10    5.40 1.39e+00 5.18e-01 1.51e+01
  angle pdb=" C4'  DC J  82 "
        pdb=" C3'  DC J  82 "
        pdb=" O3'  DC J  82 "
      ideal   model   delta    sigma   weight residual
     110.00  104.27    5.73 1.50e+00 4.44e-01 1.46e+01
  angle pdb=" C3'  DT J 106 "
        pdb=" O3'  DT J 106 "
        pdb=" P    DG J 107 "
      ideal   model   delta    sigma   weight residual
     120.20  125.30   -5.10 1.50e+00 4.44e-01 1.16e+01
  angle pdb=" N   ILE B  26 "
        pdb=" CA  ILE B  26 "
        pdb=" C   ILE B  26 "
      ideal   model   delta    sigma   weight residual
     112.50  107.99    4.51 1.39e+00 5.18e-01 1.05e+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: 1790
       0.059 -    0.118: 418
       0.118 -    0.177: 51
       0.177 -    0.236: 1
       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      2.42    2.18    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C4'  DA J  83 "
            pdb=" C5'  DA J  83 "
            pdb=" O4'  DA J  83 "
            pdb=" C3'  DA J  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.31   -0.22 2.00e-01 2.50e+01 1.21e+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:             2.310
  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:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.610
  Find NCS groups from input model:        0.060
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
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   0.072  13650  Z= 0.350
  Angle     :  0.840   8.228  19865  Z= 0.523
  Chirality :  0.050   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
  covalent geometry    : bond        0.00792 (13650)
  covalent geometry    : angle       0.83954 (19865)
  hydrogen bonds       : bond        0.14041 (  700)
  hydrogen bonds       : angle       6.28309 ( 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  : 0.323 
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: 0.8093 (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: 0.8656 (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: 0.7851 (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: 0.2031
  time to fit residues: 47.6724
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  : 0.300 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 97 optimal weight:    2.9990
   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:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3889 r_free = 0.3889 target = 0.157021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107102 restraints weight = 17681.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.17
r_work: 0.2986 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13650  Z= 0.160
  Angle     :  0.545   5.451  19865  Z= 0.331
  Chirality :  0.033   0.151   2262
  Planarity :  0.004   0.044   1368
  Dihedral  : 32.354 179.062   4452
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.12 %
    Favored  : 89.92 %
  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:  1.26 (0.29), residues: 736
  helix:  1.55 (0.21), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.16 (0.37), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.004   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13650)
  covalent geometry    : angle       0.54481 (19865)
  hydrogen bonds       : bond        0.04959 (  700)
  hydrogen bonds       : angle       2.99036 ( 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
  151 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.268 
Fit side-chains
REVERT: C   20 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8719 (ttm170)
REVERT: D   30 ARG cc_start: 0.7544 (mtt180) cc_final: 0.6843 (ptm160)
REVERT: D   37 TYR cc_start: 0.9213 (m-80) cc_final: 0.8929 (m-80)
REVERT: D   65 ASP cc_start: 0.9184 (t0) cc_final: 0.8969 (t0)
REVERT: D   80 TYR cc_start: 0.8534 (m-10) cc_final: 0.7537 (m-10)
REVERT: D  113 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8529 (tttp)
REVERT: D  116 THR cc_start: 0.8761 (m) cc_final: 0.8222 (p)
REVERT: D  117 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8654 (ttmt)
REVERT: E   90 MET cc_start: 0.8785 (tpp) cc_final: 0.8355 (mmm)
REVERT: E  120 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7985 (mtp)
REVERT: F   35 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8338 (mtm110)
REVERT: F   68 ASP cc_start: 0.9335 (m-30) cc_final: 0.9027 (m-30)
REVERT: G   35 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7938 (mtm110)
REVERT: G   36 LYS cc_start: 0.8700 (pttp) cc_final: 0.8092 (mmmt)
REVERT: G   75 LYS cc_start: 0.8480 (mttt) cc_final: 0.8234 (mtpt)
REVERT: G   95 LYS cc_start: 0.9052 (tptt) cc_final: 0.8742 (tptt)
REVERT: H   64 ASN cc_start: 0.9157 (m-40) cc_final: 0.8830 (m-40)
REVERT: H   99 LEU cc_start: 0.9418 (mt) cc_final: 0.9207 (mt)
REVERT: H  117 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8349 (ttmt)
  outliers start: 6
  outliers final: 3
  residues processed: 146
  average time/residue: 0.1342
  time to fit residues: 26.4545
Evaluate side-chains
  132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 81 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
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 = 0.3897 r_free = 0.3897 target = 0.157637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107873 restraints weight = 17983.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.14
r_work: 0.3050 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13650  Z= 0.146
  Angle     :  0.507   5.409  19865  Z= 0.310
  Chirality :  0.031   0.129   2262
  Planarity :  0.004   0.041   1368
  Dihedral  : 31.770 179.091   4452
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.24 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.74 (0.30), residues: 736
  helix:  2.70 (0.21), residues: 535
  sheet:  None (None), residues: 0
  loop : -0.74 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  42 
 TYR   0.007   0.001   TYR G  57 
 PHE   0.008   0.001   PHE F 100 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13650)
  covalent geometry    : angle       0.50702 (19865)
  hydrogen bonds       : bond        0.04360 (  700)
  hydrogen bonds       : angle       2.75703 ( 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
  147 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.9057 (tp) cc_final: 0.8781 (tp)
REVERT: C   20 ARG cc_start: 0.8967 (ttm170) cc_final: 0.8757 (ttm170)
REVERT: D   30 ARG cc_start: 0.7691 (mtt180) cc_final: 0.6724 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9274 (m-80) cc_final: 0.8973 (m-80)
REVERT: D   65 ASP cc_start: 0.9177 (t0) cc_final: 0.8894 (t0)
REVERT: D   80 TYR cc_start: 0.8395 (m-10) cc_final: 0.7294 (m-10)
REVERT: D  113 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8535 (tttp)
REVERT: D  116 THR cc_start: 0.8862 (m) cc_final: 0.8274 (p)
REVERT: E   90 MET cc_start: 0.8696 (tpp) cc_final: 0.8289 (mmm)
REVERT: E  129 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7890 (tpt90)
REVERT: F   35 ARG cc_start: 0.8722 (mtm180) cc_final: 0.8332 (mtm110)
REVERT: F   84 MET cc_start: 0.9159 (mmp) cc_final: 0.8946 (mmm)
REVERT: G   35 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7990 (mtm110)
REVERT: G   36 LYS cc_start: 0.8613 (pttp) cc_final: 0.8122 (mmmt)
REVERT: G   75 LYS cc_start: 0.8552 (mttt) cc_final: 0.8324 (mtpt)
REVERT: G   95 LYS cc_start: 0.8979 (tptt) cc_final: 0.8687 (tptt)
REVERT: G  110 ASN cc_start: 0.8680 (t0) cc_final: 0.8356 (t0)
REVERT: H   39 TYR cc_start: 0.8556 (t80) cc_final: 0.7770 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 143
  average time/residue: 0.1539
  time to fit residues: 28.9178
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 76 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
H  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.156227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106205 restraints weight = 17805.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.13
r_work: 0.2988 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13650  Z= 0.155
  Angle     :  0.513   5.487  19865  Z= 0.310
  Chirality :  0.031   0.132   2262
  Planarity :  0.004   0.039   1368
  Dihedral  : 31.733 178.918   4452
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.60 %
    Favored  : 89.28 %
  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:  3.03 (0.30), residues: 736
  helix:  2.90 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.73 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.007   0.001   PHE C  25 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (13650)
  covalent geometry    : angle       0.51280 (19865)
  hydrogen bonds       : bond        0.04490 (  700)
  hydrogen bonds       : angle       2.74902 ( 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
  138 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.9055 (tp) cc_final: 0.8764 (tp)
REVERT: C   20 ARG cc_start: 0.9043 (ttm170) cc_final: 0.8837 (ttm170)
REVERT: D   30 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6747 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9281 (m-80) cc_final: 0.9012 (m-80)
REVERT: D   65 ASP cc_start: 0.9168 (t0) cc_final: 0.8896 (t0)
REVERT: D  113 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8562 (tttp)
REVERT: D  116 THR cc_start: 0.8835 (m) cc_final: 0.8241 (p)
REVERT: E  129 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7983 (tpt90)
REVERT: F   35 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8370 (mtm110)
REVERT: G   35 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.8022 (mtm110)
REVERT: G   36 LYS cc_start: 0.8689 (pttp) cc_final: 0.8237 (mmmt)
REVERT: G   38 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8346 (m110)
REVERT: G   75 LYS cc_start: 0.8693 (mttt) cc_final: 0.8393 (mtpt)
REVERT: G   95 LYS cc_start: 0.9035 (tptt) cc_final: 0.8805 (tptt)
REVERT: H   39 TYR cc_start: 0.8540 (t80) cc_final: 0.7654 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 135
  average time/residue: 0.1568
  time to fit residues: 27.7644
Evaluate side-chains
  129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  46 HIS
D  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.155729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106249 restraints weight = 17976.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.04
r_work: 0.3029 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13650  Z= 0.157
  Angle     :  0.505   5.455  19865  Z= 0.307
  Chirality :  0.031   0.130   2262
  Planarity :  0.004   0.037   1368
  Dihedral  : 31.523 178.999   4452
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.36 %
    Favored  : 87.68 %
  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:  3.16 (0.31), residues: 736
  helix:  3.01 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.006   0.001   PHE C  25 
 HIS   0.003   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13650)
  covalent geometry    : angle       0.50519 (19865)
  hydrogen bonds       : bond        0.04489 (  700)
  hydrogen bonds       : angle       2.70820 ( 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
  139 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.313 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.9037 (tp) cc_final: 0.8780 (tp)
REVERT: C   20 ARG cc_start: 0.9057 (ttm170) cc_final: 0.8838 (ttm170)
REVERT: D   30 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6972 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9252 (m-80) cc_final: 0.8952 (m-80)
REVERT: D   65 ASP cc_start: 0.9129 (t0) cc_final: 0.8904 (t0)
REVERT: E  129 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8045 (tpt90)
REVERT: F   35 ARG cc_start: 0.8676 (mtm180) cc_final: 0.8334 (mtm110)
REVERT: G   20 ARG cc_start: 0.8698 (ttm170) cc_final: 0.8465 (ttp80)
REVERT: G   35 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7962 (mtm110)
REVERT: G   36 LYS cc_start: 0.8459 (pttp) cc_final: 0.8160 (mmmt)
REVERT: G   38 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8338 (m110)
REVERT: G   75 LYS cc_start: 0.8703 (mttt) cc_final: 0.8489 (mtpt)
REVERT: G   95 LYS cc_start: 0.8951 (tptt) cc_final: 0.8716 (tptt)
REVERT: H   31 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8247 (ttpt)
REVERT: H   39 TYR cc_start: 0.8728 (t80) cc_final: 0.7608 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 136
  average time/residue: 0.1533
  time to fit residues: 27.5812
Evaluate side-chains
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain D residue   33 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.154808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.105266 restraints weight = 17875.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.02
r_work: 0.2992 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13650  Z= 0.164
  Angle     :  0.516   5.373  19865  Z= 0.311
  Chirality :  0.032   0.136   2262
  Planarity :  0.004   0.036   1368
  Dihedral  : 31.559 179.062   4452
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.68 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.18 (0.31), residues: 736
  helix:  3.00 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.68 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.008   0.001   PHE F 100 
 HIS   0.004   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (13650)
  covalent geometry    : angle       0.51572 (19865)
  hydrogen bonds       : bond        0.04642 (  700)
  hydrogen bonds       : angle       2.74551 ( 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
  139 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.293 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.9078 (tp) cc_final: 0.8815 (tp)
REVERT: B   88 TYR cc_start: 0.9092 (m-10) cc_final: 0.8544 (m-80)
REVERT: C   20 ARG cc_start: 0.9081 (ttm170) cc_final: 0.8855 (ttm170)
REVERT: D   30 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7045 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9245 (m-80) cc_final: 0.9008 (m-80)
REVERT: D   65 ASP cc_start: 0.9128 (t0) cc_final: 0.8895 (t0)
REVERT: E  129 ARG cc_start: 0.8455 (tpt90) cc_final: 0.8114 (tpt90)
REVERT: F   35 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8342 (mtm110)
REVERT: G   35 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7970 (mtm110)
REVERT: G   36 LYS cc_start: 0.8464 (pttp) cc_final: 0.8151 (mmmt)
REVERT: G   38 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8317 (m110)
REVERT: G   75 LYS cc_start: 0.8729 (mttt) cc_final: 0.8496 (mtpt)
REVERT: H   39 TYR cc_start: 0.8811 (t80) cc_final: 0.8439 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 135
  average time/residue: 0.1540
  time to fit residues: 27.4032
Evaluate side-chains
  133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain D residue   33 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3843 r_free = 0.3843 target = 0.153037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.103577 restraints weight = 17847.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.01
r_work: 0.2966 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13650  Z= 0.185
  Angle     :  0.531   5.471  19865  Z= 0.318
  Chirality :  0.033   0.133   2262
  Planarity :  0.004   0.035   1368
  Dihedral  : 31.607 179.278   4452
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.52 %
    Favored  : 86.56 %
  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:  3.09 (0.31), residues: 736
  helix:  2.93 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.67 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  83 
 TYR   0.014   0.001   TYR F  51 
 PHE   0.011   0.001   PHE A  78 
 HIS   0.003   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (13650)
  covalent geometry    : angle       0.53113 (19865)
  hydrogen bonds       : bond        0.04905 (  700)
  hydrogen bonds       : angle       2.82819 ( 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
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.187 
Fit side-chains
REVERT: D   30 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7034 (ptp-170)
REVERT: D   65 ASP cc_start: 0.9134 (t0) cc_final: 0.8886 (t0)
REVERT: E  129 ARG cc_start: 0.8454 (tpt90) cc_final: 0.8111 (tpt90)
REVERT: F   35 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8439 (mtm110)
REVERT: G   35 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7935 (mtm110)
REVERT: G   36 LYS cc_start: 0.8478 (pttp) cc_final: 0.8158 (mmmt)
REVERT: G   38 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8322 (m110)
REVERT: G   73 ASN cc_start: 0.8722 (t0) cc_final: 0.8521 (t0)
REVERT: G   75 LYS cc_start: 0.8700 (mttt) cc_final: 0.8490 (mtpt)
  outliers start: 12
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1476
  time to fit residues: 25.6248
Evaluate side-chains
  135 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
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   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
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:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3851 r_free = 0.3851 target = 0.153712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.103576 restraints weight = 17766.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.12
r_work: 0.2976 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13650  Z= 0.158
  Angle     :  0.521   6.254  19865  Z= 0.314
  Chirality :  0.032   0.131   2262
  Planarity :  0.004   0.086   1368
  Dihedral  : 31.589 179.244   4452
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.84 %
    Favored  : 86.56 %
  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:  3.15 (0.31), residues: 736
  helix:  2.97 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.66 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.014   0.001   TYR D  37 
 PHE   0.006   0.001   PHE D  62 
 HIS   0.002   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (13650)
  covalent geometry    : angle       0.52061 (19865)
  hydrogen bonds       : bond        0.04724 (  700)
  hydrogen bonds       : angle       2.79638 ( 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
  136 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.302 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9053 (m-10) cc_final: 0.8408 (m-80)
REVERT: D   30 ARG cc_start: 0.7976 (mtt180) cc_final: 0.6962 (ptp-170)
REVERT: D   65 ASP cc_start: 0.9168 (t0) cc_final: 0.8892 (t0)
REVERT: E  129 ARG cc_start: 0.8462 (tpt90) cc_final: 0.8118 (tpt90)
REVERT: F   35 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8426 (mtm110)
REVERT: G   35 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7955 (mtm110)
REVERT: G   36 LYS cc_start: 0.8534 (pttp) cc_final: 0.8130 (mmmt)
REVERT: G   38 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8328 (m110)
REVERT: G   75 LYS cc_start: 0.8746 (mttt) cc_final: 0.8492 (mtpt)
  outliers start: 10
  outliers final: 9
  residues processed: 131
  average time/residue: 0.1520
  time to fit residues: 26.3218
Evaluate side-chains
  135 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
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:    0.1980
   chunk 76 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 85 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.154081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.104088 restraints weight = 17832.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.12
r_work: 0.2987 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3372

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= 0.147
  Angle     :  0.514   6.247  19865  Z= 0.311
  Chirality :  0.031   0.131   2262
  Planarity :  0.004   0.060   1368
  Dihedral  : 31.570 179.183   4452
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.84 %
    Favored  : 86.56 %
  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:  3.22 (0.31), residues: 736
  helix:  3.02 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.63 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.009   0.001   PHE A  78 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13650)
  covalent geometry    : angle       0.51432 (19865)
  hydrogen bonds       : bond        0.04631 (  700)
  hydrogen bonds       : angle       2.77768 ( 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
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.249 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9058 (m-10) cc_final: 0.8446 (m-80)
REVERT: D   30 ARG cc_start: 0.7983 (mtt180) cc_final: 0.6961 (ptp-170)
REVERT: D   65 ASP cc_start: 0.9171 (t0) cc_final: 0.8884 (t0)
REVERT: E  129 ARG cc_start: 0.8473 (tpt90) cc_final: 0.8143 (tpt90)
REVERT: F   35 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8422 (mtm110)
REVERT: G   35 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7935 (mtm110)
REVERT: G   36 LYS cc_start: 0.8520 (pttp) cc_final: 0.8132 (mmmt)
REVERT: G   38 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8318 (m110)
REVERT: G   75 LYS cc_start: 0.8730 (mttt) cc_final: 0.8480 (mtpt)
  outliers start: 10
  outliers final: 9
  residues processed: 131
  average time/residue: 0.1455
  time to fit residues: 25.3129
Evaluate side-chains
  136 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
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 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0770
   chunk 92 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0470
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.153969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.104659 restraints weight = 17859.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.01
r_work: 0.2996 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.3381

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= 0.149
  Angle     :  0.513   6.115  19865  Z= 0.310
  Chirality :  0.031   0.131   2262
  Planarity :  0.004   0.058   1368
  Dihedral  : 31.558 179.177   4452
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.68 %
    Favored  : 86.56 %
  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:  3.21 (0.31), residues: 736
  helix:  3.02 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.62 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  83 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.007   0.001   PHE A  78 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13650)
  covalent geometry    : angle       0.51276 (19865)
  hydrogen bonds       : bond        0.04615 (  700)
  hydrogen bonds       : angle       2.76830 ( 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
  138 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.302 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9053 (m-10) cc_final: 0.8442 (m-80)
REVERT: D   30 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7023 (ptp-170)
REVERT: D   65 ASP cc_start: 0.9126 (t0) cc_final: 0.8882 (t0)
REVERT: E  129 ARG cc_start: 0.8458 (tpt90) cc_final: 0.8138 (tpt90)
REVERT: F   35 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8433 (mtm110)
REVERT: G   35 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7930 (mtm110)
REVERT: G   36 LYS cc_start: 0.8473 (pttp) cc_final: 0.8161 (mmmt)
REVERT: G   38 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8310 (m110)
REVERT: G   75 LYS cc_start: 0.8733 (mttt) cc_final: 0.8511 (mtpt)
  outliers start: 11
  outliers final: 10
  residues processed: 132
  average time/residue: 0.1527
  time to fit residues: 26.5218
Evaluate side-chains
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
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:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.102350 restraints weight = 17758.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.01
r_work: 0.2951 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13650  Z= 0.205
  Angle     :  0.548   5.808  19865  Z= 0.327
  Chirality :  0.034   0.143   2262
  Planarity :  0.004   0.033   1368
  Dihedral  : 31.680 179.609   4452
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.16 %
    Favored  : 86.24 %
  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:  2.96 (0.31), residues: 736
  helix:  2.87 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.84 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.008   0.002   PHE A  78 
 HIS   0.004   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (13650)
  covalent geometry    : angle       0.54782 (19865)
  hydrogen bonds       : bond        0.05164 (  700)
  hydrogen bonds       : angle       2.88710 ( 1796)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3217.86 seconds
wall clock time: 55 minutes 23.91 seconds (3323.91 seconds total)