Starting phenix.real_space_refine
on Wed Sep 17 21:26:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3z_62034/09_2025/9k3z_62034.map"
  }
  resolution = 2.75
  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=   0.050
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     289      5.49       5
     S      10      5.16       5
     C    6565      2.51       5
     N    2174      2.21       5
     O    2776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11814
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.59, per 1000 atoms: 0.22
  Number of scatterers: 11814
  At special positions: 0
  Unit cell: (118.992, 78.256, 114.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     289     15.00
     O    2776      8.00
     N    2174      7.00
     C    6565      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: 0.71
  Conformation dependent library (CDL) restraints added in 280.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      75.3% alpha, 2.7% beta
      144 base pairs and 264 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.507A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'C' and resid 37 through 49
    Processing helix  chain 'C' and resid 56 through 85
    Processing helix  chain 'C' and resid 91 through 101
    Processing helix  chain 'C' and resid 102 through 109
    Processing helix  chain 'C' and resid 123 through 127
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 147
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 27 through 32
    Processing helix  chain 'G' and resid 37 through 49
    Processing helix  chain 'G' and resid 56 through 85
    Processing helix  chain 'G' and resid 91 through 102
    Processing helix  chain 'G' and resid 102 through 109
    Processing helix  chain 'G' and resid 123 through 127
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.876A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.607A  pdb=" N   ARG C  54 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113
      removed outlier: 6.380A  pdb=" N   THR C 112 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.021A  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 54 through 55
      removed outlier: 6.642A  pdb=" N   ARG G  54 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90

    424 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      346 hydrogen bonds
      688 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      264 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.05 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: 1980
        1.33 -     1.45: 4258
        1.45 -     1.57: 5786
        1.57 -     1.69: 577
        1.69 -     1.81: 18
  Bond restraints: 12619
  Sorted by residual:
  bond pdb=" O3'  DG I -26 "
       pdb=" P    DT I -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.666 -0.059 1.50e-02 4.44e+03 1.54e+01
  bond pdb=" O3'  DA J -46 "
       pdb=" P    DA J -45 "
    ideal  model  delta    sigma   weight residual
    1.607  1.665 -0.058 1.50e-02 4.44e+03 1.48e+01
  bond pdb=" O3'  DT I -16 "
       pdb=" P    DC I -15 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.50e-02 4.44e+03 1.34e+01
  bond pdb=" O3'  DC J -24 "
       pdb=" P    DC J -23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.652 -0.045 1.50e-02 4.44e+03 9.03e+00
  bond pdb=" O3'  DC I -36 "
       pdb=" P    DG I -35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.640 -0.033 1.50e-02 4.44e+03 4.74e+00
  ... (remaining 12614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 17081
        1.10 -     2.19: 962
        2.19 -     3.29: 212
        3.29 -     4.39: 22
        4.39 -     5.48: 8
  Bond angle restraints: 18285
  Sorted by residual:
  angle pdb=" O3'  DC I -28 "
        pdb=" C3'  DC I -28 "
        pdb=" C2'  DC I -28 "
      ideal   model   delta    sigma   weight residual
     111.50  106.02    5.48 1.50e+00 4.44e-01 1.34e+01
  angle pdb=" O3'  DC I -36 "
        pdb=" C3'  DC I -36 "
        pdb=" C2'  DC I -36 "
      ideal   model   delta    sigma   weight residual
     111.50  106.07    5.43 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" O3'  DG J -48 "
        pdb=" C3'  DG J -48 "
        pdb=" C2'  DG J -48 "
      ideal   model   delta    sigma   weight residual
     111.50  106.19    5.31 1.50e+00 4.44e-01 1.25e+01
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  106.35    5.15 1.50e+00 4.44e-01 1.18e+01
  angle pdb=" O3'  DG J -47 "
        pdb=" C3'  DG J -47 "
        pdb=" C2'  DG J -47 "
      ideal   model   delta    sigma   weight residual
     111.50  107.12    4.38 1.50e+00 4.44e-01 8.53e+00
  ... (remaining 18280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.95: 4227
       18.95 -    37.89: 1269
       37.89 -    56.84: 1231
       56.84 -    75.79: 182
       75.79 -    94.73: 8
  Dihedral angle restraints: 6917
    sinusoidal: 4771
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CG  ARG E 129 "
           pdb=" CD  ARG E 129 "
           pdb=" NE  ARG E 129 "
           pdb=" CZ  ARG E 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.26  -42.74     2      1.50e+01 4.44e-03 9.83e+00
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.51  -42.49     2      1.50e+01 4.44e-03 9.73e+00
  dihedral pdb=" CA  ARG F  23 "
           pdb=" CB  ARG F  23 "
           pdb=" CG  ARG F  23 "
           pdb=" CD  ARG F  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.93  -59.93     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 6914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1551
       0.036 -    0.072: 442
       0.072 -    0.108: 74
       0.108 -    0.144: 23
       0.144 -    0.180: 7
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" C3'  DC I -28 "
            pdb=" C4'  DC I -28 "
            pdb=" O3'  DC I -28 "
            pdb=" C2'  DC I -28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.84    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" C3'  DG J -47 "
            pdb=" C4'  DG J -47 "
            pdb=" O3'  DG J -47 "
            pdb=" C2'  DG J -47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.83    0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" C3'  DG J -48 "
            pdb=" C4'  DG J -48 "
            pdb=" O3'  DG J -48 "
            pdb=" C2'  DG J -48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.83    0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 2094 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  57 "    0.023 2.00e-02 2.50e+03   1.02e-02 2.84e+00
        pdb=" N9   DA I  57 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  57 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  57 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  57 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  57 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  57 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  17 "   -0.019 2.00e-02 2.50e+03   1.00e-02 2.26e+00
        pdb=" N1   DC I  17 "    0.016 2.00e-02 2.50e+03
        pdb=" C2   DC I  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DC I  17 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I  17 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I  17 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DC I  17 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO B  32 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1099
        2.74 -     3.28: 10207
        3.28 -     3.82: 23398
        3.82 -     4.36: 28618
        4.36 -     4.90: 40527
  Nonbonded interactions: 103849
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG G  48 "
            pdb=" OE1 GLU H  94 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NZ  LYS F  59 "
            pdb=" OE2 GLU F  63 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OG  SER C  29 "
            pdb=" O   PHE C  36 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER G  29 "
            pdb=" O   PHE G  36 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NZ  LYS B  59 "
            pdb=" OE2 GLU B  63 "
     model   vdw
     2.233 3.120
  ... (remaining 103844 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
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=0.00 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:             1.500
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.280
  Find NCS groups from input model:        0.210
  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:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12619  Z= 0.197
  Angle     :  0.589   5.482  18285  Z= 0.366
  Chirality :  0.036   0.180   2097
  Planarity :  0.003   0.036   1296
  Dihedral  : 29.151  94.731   5529
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 22.19 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.30), residues: 728
  helix:  2.34 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.00 (0.40), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  43 
 TYR   0.009   0.001   TYR D  63 
 PHE   0.007   0.001   PHE D  88 
 HIS   0.002   0.001   HIS C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12619)
  covalent geometry    : angle       0.58884 (18285)
  hydrogen bonds       : bond        0.11994 (  770)
  hydrogen bonds       : angle       4.18541 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 217
  time to evaluate  : 0.299 
Fit side-chains
REVERT: C   48 ARG cc_start: 0.8476 (ttm170) cc_final: 0.8021 (tpp80)
REVERT: C   62 TYR cc_start: 0.8840 (t80) cc_final: 0.8450 (t80)
REVERT: D  147 SER cc_start: 0.8233 (m) cc_final: 0.7963 (p)
REVERT: G   62 TYR cc_start: 0.8809 (t80) cc_final: 0.8601 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 220
  average time/residue: 0.6841
  time to fit residues: 159.9886
Evaluate side-chains
  173 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain F residue   49 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
A 113 HIS
B  75 HIS
B  93 GLN
D 132 HIS
E  85 GLN
E 108 ASN
E 125 GLN
F  75 HIS
F  93 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.070814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.048563 restraints weight = 37579.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 1.91
r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12619  Z= 0.184
  Angle     :  0.585   5.679  18285  Z= 0.357
  Chirality :  0.035   0.151   2097
  Planarity :  0.004   0.032   1296
  Dihedral  : 31.305  88.423   4072
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.60 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.29 (0.30), residues: 728
  helix:  2.71 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.34 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 105 
 TYR   0.011   0.001   TYR G  69 
 PHE   0.010   0.001   PHE D  93 
 HIS   0.003   0.001   HIS C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12619)
  covalent geometry    : angle       0.58504 (18285)
  hydrogen bonds       : bond        0.04718 (  770)
  hydrogen bonds       : angle       3.02748 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8009 (pt0) cc_final: 0.7737 (pm20)
REVERT: C  102 ASP cc_start: 0.9017 (t0) cc_final: 0.8767 (t0)
REVERT: C  104 GLU cc_start: 0.9245 (mm-30) cc_final: 0.9023 (mm-30)
REVERT: D  128 GLU cc_start: 0.8511 (tp30) cc_final: 0.8217 (tp30)
REVERT: D  129 LEU cc_start: 0.9529 (tp) cc_final: 0.9318 (tp)
REVERT: E   59 GLU cc_start: 0.8052 (pt0) cc_final: 0.7842 (pm20)
REVERT: E  120 MET cc_start: 0.8734 (mtp) cc_final: 0.8417 (mtt)
REVERT: G   48 ARG cc_start: 0.9028 (tpp80) cc_final: 0.8692 (tpp80)
REVERT: G   88 LYS cc_start: 0.9364 (mtmt) cc_final: 0.9147 (mtmt)
REVERT: H   94 GLU cc_start: 0.9245 (tp30) cc_final: 0.9023 (tp30)
REVERT: H  128 GLU cc_start: 0.8487 (tp30) cc_final: 0.8148 (tp30)
  outliers start: 19
  outliers final: 7
  residues processed: 184
  average time/residue: 0.6454
  time to fit residues: 126.8492
Evaluate side-chains
  160 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue   57 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  35 GLN
D  98 GLN
G  35 GLN
H  98 GLN
H 132 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.067771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.045140 restraints weight = 37940.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 1.97
r_work: 0.2606 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12619  Z= 0.258
  Angle     :  0.613   6.574  18285  Z= 0.372
  Chirality :  0.037   0.157   2097
  Planarity :  0.004   0.030   1296
  Dihedral  : 31.746  91.206   4069
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.83 %
    Favored  : 72.51 %
  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 aren not related in a simple way.
  whole:  3.38 (0.30), residues: 728
  helix:  2.79 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.30 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 105 
 TYR   0.011   0.001   TYR H  60 
 PHE   0.008   0.001   PHE C  36 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 (12619)
  covalent geometry    : angle       0.61263 (18285)
  hydrogen bonds       : bond        0.05274 (  770)
  hydrogen bonds       : angle       3.16076 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8514 (pt0) cc_final: 0.8286 (pm20)
REVERT: B   59 LYS cc_start: 0.9170 (tttm) cc_final: 0.8959 (ttmm)
REVERT: B   93 GLN cc_start: 0.9239 (mm-40) cc_final: 0.9013 (mp10)
REVERT: B   95 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7430 (mmm160)
REVERT: C   46 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8863 (mtmm)
REVERT: C  102 ASP cc_start: 0.9006 (t0) cc_final: 0.8651 (t0)
REVERT: C  104 GLU cc_start: 0.9275 (mm-30) cc_final: 0.9007 (mm-30)
REVERT: D   91 ASP cc_start: 0.9419 (t0) cc_final: 0.9007 (t0)
REVERT: D  101 SER cc_start: 0.9652 (m) cc_final: 0.9380 (p)
REVERT: D  128 GLU cc_start: 0.8620 (tp30) cc_final: 0.8303 (tp30)
REVERT: F   93 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8995 (mp10)
REVERT: F   95 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7494 (mmm160)
REVERT: G   46 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8940 (mtpp)
REVERT: G   48 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8690 (tpp80)
REVERT: G  102 ASP cc_start: 0.8852 (t0) cc_final: 0.8474 (t0)
REVERT: H   91 ASP cc_start: 0.9479 (t0) cc_final: 0.9064 (t0)
REVERT: H   94 GLU cc_start: 0.9231 (tp30) cc_final: 0.8954 (tp30)
  outliers start: 29
  outliers final: 11
  residues processed: 171
  average time/residue: 0.6837
  time to fit residues: 124.2182
Evaluate side-chains
  163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   85 MET
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   87 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 69 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 87 optimal weight:    8.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C  35 GLN
D  70 GLN
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.070391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.047925 restraints weight = 37704.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.96
r_work: 0.2705 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12619  Z= 0.150
  Angle     :  0.567   6.448  18285  Z= 0.347
  Chirality :  0.034   0.160   2097
  Planarity :  0.004   0.031   1296
  Dihedral  : 31.150  85.394   4069
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.79 %
    Favored  : 73.15 %
  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 aren not related in a simple way.
  whole:  3.73 (0.30), residues: 728
  helix:  3.08 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.39 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 105 
 TYR   0.010   0.001   TYR G  69 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12619)
  covalent geometry    : angle       0.56697 (18285)
  hydrogen bonds       : bond        0.03988 (  770)
  hydrogen bonds       : angle       2.79824 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.8774 (p0) cc_final: 0.8532 (p0)
REVERT: B   79 LYS cc_start: 0.9290 (mttp) cc_final: 0.8888 (mtmt)
REVERT: C   26 ILE cc_start: 0.9133 (mp) cc_final: 0.8657 (tt)
REVERT: C  102 ASP cc_start: 0.9047 (t0) cc_final: 0.8695 (t0)
REVERT: C  104 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8990 (mm-30)
REVERT: D   91 ASP cc_start: 0.9396 (t0) cc_final: 0.9024 (t0)
REVERT: D  129 LEU cc_start: 0.9471 (tp) cc_final: 0.9262 (tp)
REVERT: F   93 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8895 (mp10)
REVERT: G   46 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8897 (mtpp)
REVERT: G   48 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8712 (tpp80)
REVERT: G   88 LYS cc_start: 0.9395 (mtmt) cc_final: 0.9149 (mtmt)
REVERT: G  102 ASP cc_start: 0.8719 (t0) cc_final: 0.8423 (t0)
REVERT: G  104 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8987 (mm-30)
REVERT: H   91 ASP cc_start: 0.9399 (t0) cc_final: 0.9038 (t0)
REVERT: H   94 GLU cc_start: 0.9222 (tp30) cc_final: 0.8922 (tp30)
REVERT: H  128 GLU cc_start: 0.8190 (tp30) cc_final: 0.7919 (tp30)
  outliers start: 19
  outliers final: 5
  residues processed: 191
  average time/residue: 0.6379
  time to fit residues: 130.0806
Evaluate side-chains
  169 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E 113 HIS
G  35 GLN
H  70 GLN
H  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.069341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.047149 restraints weight = 37854.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.94
r_work: 0.2674 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12619  Z= 0.187
  Angle     :  0.575   6.425  18285  Z= 0.351
  Chirality :  0.034   0.153   2097
  Planarity :  0.004   0.032   1296
  Dihedral  : 31.273  87.114   4069
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 25.72 %
    Favored  : 71.22 %
  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 aren not related in a simple way.
  whole:  3.78 (0.30), residues: 728
  helix:  3.10 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.42 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.010   0.001   TYR C  62 
 PHE   0.006   0.001   PHE B  61 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (12619)
  covalent geometry    : angle       0.57454 (18285)
  hydrogen bonds       : bond        0.04308 (  770)
  hydrogen bonds       : angle       2.84270 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B   95 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7314 (mmm160)
REVERT: C   26 ILE cc_start: 0.9077 (mp) cc_final: 0.8638 (tt)
REVERT: C  102 ASP cc_start: 0.9055 (t0) cc_final: 0.8687 (t0)
REVERT: C  104 GLU cc_start: 0.9254 (mm-30) cc_final: 0.9011 (mm-30)
REVERT: D   91 ASP cc_start: 0.9381 (t0) cc_final: 0.9007 (t0)
REVERT: D  129 LEU cc_start: 0.9477 (tp) cc_final: 0.9270 (tp)
REVERT: F   95 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7421 (mmm160)
REVERT: G   48 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8527 (tpp80)
REVERT: G  102 ASP cc_start: 0.8741 (t0) cc_final: 0.8209 (t0)
REVERT: G  104 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9034 (mm-30)
REVERT: H   91 ASP cc_start: 0.9399 (t0) cc_final: 0.9037 (t0)
REVERT: H   94 GLU cc_start: 0.9221 (tp30) cc_final: 0.8790 (tp30)
REVERT: H  128 GLU cc_start: 0.8305 (tp30) cc_final: 0.8009 (tp30)
  outliers start: 19
  outliers final: 6
  residues processed: 169
  average time/residue: 0.7347
  time to fit residues: 131.8153
Evaluate side-chains
  163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  72 HIS
E  68 GLN
G  35 GLN
H  70 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.070068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.047511 restraints weight = 37621.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 1.92
r_work: 0.2694 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12619  Z= 0.156
  Angle     :  0.569   6.399  18285  Z= 0.347
  Chirality :  0.034   0.152   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 31.178  87.286   4069
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.49 %
    Favored  : 69.94 %
  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 aren not related in a simple way.
  whole:  3.84 (0.30), residues: 728
  helix:  3.15 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.46 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.014   0.001   TYR G  62 
 PHE   0.006   0.001   PHE F  61 
 HIS   0.004   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12619)
  covalent geometry    : angle       0.56915 (18285)
  hydrogen bonds       : bond        0.03963 (  770)
  hydrogen bonds       : angle       2.75953 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.305 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9312 (mttp) cc_final: 0.8895 (ttmm)
REVERT: B   95 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7280 (mmm160)
REVERT: C   26 ILE cc_start: 0.9077 (mp) cc_final: 0.8665 (tt)
REVERT: C  102 ASP cc_start: 0.9054 (t0) cc_final: 0.8706 (t0)
REVERT: C  104 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9028 (mm-30)
REVERT: D   91 ASP cc_start: 0.9378 (t0) cc_final: 0.9016 (t0)
REVERT: F   95 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7401 (mmm160)
REVERT: G   46 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8881 (mtpp)
REVERT: G   48 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8820 (tpp80)
REVERT: G  102 ASP cc_start: 0.8727 (t0) cc_final: 0.8194 (t0)
REVERT: G  104 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9040 (mm-30)
REVERT: H   59 THR cc_start: 0.9222 (p) cc_final: 0.9015 (t)
REVERT: H   91 ASP cc_start: 0.9393 (t0) cc_final: 0.9038 (t0)
REVERT: H   94 GLU cc_start: 0.9220 (tp30) cc_final: 0.8991 (tp30)
REVERT: H  128 GLU cc_start: 0.8219 (tp30) cc_final: 0.7971 (tp30)
  outliers start: 16
  outliers final: 4
  residues processed: 169
  average time/residue: 0.7057
  time to fit residues: 126.8353
Evaluate side-chains
  163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue   57 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  72 HIS
D  98 GLN
G  35 GLN
H  70 GLN
H  98 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.069181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.047113 restraints weight = 37258.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.92
r_work: 0.2674 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12619  Z= 0.190
  Angle     :  0.585   6.530  18285  Z= 0.354
  Chirality :  0.035   0.154   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 31.236  87.130   4069
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 27.17 %
    Favored  : 69.94 %
  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 aren not related in a simple way.
  whole:  3.82 (0.30), residues: 728
  helix:  3.12 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.50 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 105 
 TYR   0.016   0.002   TYR C  62 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (12619)
  covalent geometry    : angle       0.58469 (18285)
  hydrogen bonds       : bond        0.04303 (  770)
  hydrogen bonds       : angle       2.83607 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.271 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9297 (mttp) cc_final: 0.8901 (ttmm)
REVERT: B   95 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7282 (mmm160)
REVERT: C   26 ILE cc_start: 0.9097 (mp) cc_final: 0.8711 (tt)
REVERT: C   84 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8920 (t0)
REVERT: C  102 ASP cc_start: 0.9043 (t0) cc_final: 0.8693 (t0)
REVERT: D   91 ASP cc_start: 0.9383 (t0) cc_final: 0.9019 (t0)
REVERT: F   95 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7418 (mmm160)
REVERT: G   46 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8951 (mtpp)
REVERT: G   48 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8812 (tpp80)
REVERT: G   88 LYS cc_start: 0.9408 (mtmt) cc_final: 0.8874 (ptmt)
REVERT: G  102 ASP cc_start: 0.8761 (t0) cc_final: 0.8162 (t0)
REVERT: G  104 GLU cc_start: 0.9245 (mm-30) cc_final: 0.9023 (mm-30)
REVERT: H   59 THR cc_start: 0.9209 (p) cc_final: 0.8974 (t)
REVERT: H   91 ASP cc_start: 0.9393 (t0) cc_final: 0.9043 (t0)
REVERT: H   94 GLU cc_start: 0.9212 (tp30) cc_final: 0.8952 (tp30)
REVERT: H  128 GLU cc_start: 0.8334 (tp30) cc_final: 0.8076 (tp30)
  outliers start: 18
  outliers final: 6
  residues processed: 161
  average time/residue: 0.7419
  time to fit residues: 126.7221
Evaluate side-chains
  161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 152
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   84 ASP
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  72 HIS
D 132 HIS
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.069627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.046915 restraints weight = 37382.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 1.93
r_work: 0.2682 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12619  Z= 0.170
  Angle     :  0.583   6.842  18285  Z= 0.353
  Chirality :  0.034   0.156   2097
  Planarity :  0.004   0.038   1296
  Dihedral  : 31.222  87.838   4069
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 28.62 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.78 (0.31), residues: 728
  helix:  3.04 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.58 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 105 
 TYR   0.016   0.002   TYR C  62 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (12619)
  covalent geometry    : angle       0.58296 (18285)
  hydrogen bonds       : bond        0.04181 (  770)
  hydrogen bonds       : angle       2.80790 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9303 (mttp) cc_final: 0.8904 (ttmm)
REVERT: B   95 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7251 (mmm160)
REVERT: C   26 ILE cc_start: 0.9101 (mp) cc_final: 0.8707 (tt)
REVERT: C   84 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8923 (t0)
REVERT: C  102 ASP cc_start: 0.9011 (t0) cc_final: 0.8690 (t0)
REVERT: D   91 ASP cc_start: 0.9379 (t0) cc_final: 0.9020 (t0)
REVERT: F   95 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7408 (mmm160)
REVERT: G   46 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8940 (mtpp)
REVERT: G   48 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8594 (tpp80)
REVERT: G   88 LYS cc_start: 0.9407 (mtmt) cc_final: 0.8823 (ptmt)
REVERT: G  102 ASP cc_start: 0.8742 (t0) cc_final: 0.8180 (t0)
REVERT: G  104 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: H   91 ASP cc_start: 0.9391 (t0) cc_final: 0.9035 (t0)
REVERT: H   94 GLU cc_start: 0.9218 (tp30) cc_final: 0.8798 (tp30)
REVERT: H  128 GLU cc_start: 0.8317 (tp30) cc_final: 0.8056 (tp30)
  outliers start: 17
  outliers final: 7
  residues processed: 163
  average time/residue: 0.7584
  time to fit residues: 131.2931
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   84 ASP
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   48 ARG
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  98 GLN
E  68 GLN
H  98 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.068203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.045978 restraints weight = 37035.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.92
r_work: 0.2637 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  12619  Z= 0.214
  Angle     :  0.607   7.290  18285  Z= 0.365
  Chirality :  0.036   0.162   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.410  89.395   4069
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 29.10 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.74 (0.31), residues: 728
  helix:  3.00 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.61 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 105 
 TYR   0.016   0.002   TYR C  62 
 PHE   0.007   0.001   PHE B  61 
 HIS   0.005   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (12619)
  covalent geometry    : angle       0.60663 (18285)
  hydrogen bonds       : bond        0.04690 (  770)
  hydrogen bonds       : angle       2.90748 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9289 (mttp) cc_final: 0.8912 (ttmm)
REVERT: B   95 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7294 (mmm160)
REVERT: C   26 ILE cc_start: 0.9113 (mp) cc_final: 0.8738 (tt)
REVERT: C   48 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8705 (tpp80)
REVERT: C  102 ASP cc_start: 0.9035 (t0) cc_final: 0.8696 (t0)
REVERT: C  104 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9035 (mm-30)
REVERT: D   91 ASP cc_start: 0.9381 (t0) cc_final: 0.9006 (t0)
REVERT: D  128 GLU cc_start: 0.8302 (tp30) cc_final: 0.8074 (tp30)
REVERT: F   95 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7457 (mmm160)
REVERT: G   46 LYS cc_start: 0.9229 (mtpp) cc_final: 0.9024 (mtpp)
REVERT: G   48 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8617 (tpp80)
REVERT: G   88 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9129 (mtmt)
REVERT: G  102 ASP cc_start: 0.8780 (t0) cc_final: 0.8172 (t0)
REVERT: H   91 ASP cc_start: 0.9411 (t0) cc_final: 0.9046 (t0)
REVERT: H   94 GLU cc_start: 0.9196 (tp30) cc_final: 0.8761 (tp30)
  outliers start: 15
  outliers final: 5
  residues processed: 159
  average time/residue: 0.7550
  time to fit residues: 127.0218
Evaluate side-chains
  159 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   48 ARG
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  70 GLN
D  72 HIS
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.068595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.046434 restraints weight = 37536.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.94
r_work: 0.2651 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12619  Z= 0.177
  Angle     :  0.609   7.858  18285  Z= 0.365
  Chirality :  0.035   0.165   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 31.401  89.045   4069
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 30.39 %
    Favored  : 68.01 %
  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 aren not related in a simple way.
  whole:  3.72 (0.31), residues: 728
  helix:  2.99 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.62 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 105 
 TYR   0.016   0.002   TYR C  62 
 PHE   0.013   0.001   PHE H  88 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (12619)
  covalent geometry    : angle       0.60855 (18285)
  hydrogen bonds       : bond        0.04465 (  770)
  hydrogen bonds       : angle       2.87201 ( 1936)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9294 (mttp) cc_final: 0.8915 (ttmm)
REVERT: B   95 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7380 (mmm160)
REVERT: C   26 ILE cc_start: 0.9105 (mp) cc_final: 0.8735 (tt)
REVERT: C   48 ARG cc_start: 0.9182 (tpp-160) cc_final: 0.8710 (tpp80)
REVERT: C  102 ASP cc_start: 0.9022 (t0) cc_final: 0.8723 (t0)
REVERT: C  104 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: D   91 ASP cc_start: 0.9393 (t0) cc_final: 0.9020 (t0)
REVERT: D  128 GLU cc_start: 0.8274 (tp30) cc_final: 0.8026 (tp30)
REVERT: F   59 LYS cc_start: 0.9132 (tttm) cc_final: 0.8918 (tttp)
REVERT: F   95 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7453 (mmm160)
REVERT: G   46 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8903 (mtpp)
REVERT: G   48 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8612 (tpp80)
REVERT: G   88 LYS cc_start: 0.9386 (mtmt) cc_final: 0.8718 (ptmm)
REVERT: G  102 ASP cc_start: 0.8772 (t0) cc_final: 0.8183 (t0)
REVERT: H   91 ASP cc_start: 0.9411 (t0) cc_final: 0.9054 (t0)
REVERT: H   94 GLU cc_start: 0.9198 (tp30) cc_final: 0.8754 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 160
  average time/residue: 0.7273
  time to fit residues: 123.3963
Evaluate side-chains
  160 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   48 ARG
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  98 GLN
E  68 GLN
H  98 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.069701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.047083 restraints weight = 37516.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 1.96
r_work: 0.2684 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12619  Z= 0.161
  Angle     :  0.599   7.879  18285  Z= 0.360
  Chirality :  0.035   0.206   2097
  Planarity :  0.004   0.046   1296
  Dihedral  : 31.196  87.092   4069
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 29.90 %
    Favored  : 68.33 %
  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 aren not related in a simple way.
  whole:  3.74 (0.31), residues: 728
  helix:  3.00 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.62 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 105 
 TYR   0.015   0.002   TYR C  62 
 PHE   0.007   0.001   PHE B  61 
 HIS   0.003   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12619)
  covalent geometry    : angle       0.59927 (18285)
  hydrogen bonds       : bond        0.03986 (  770)
  hydrogen bonds       : angle       2.79019 ( 1936)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3721.25 seconds
wall clock time: 63 minutes 59.18 seconds (3839.18 seconds total)