Starting phenix.real_space_refine
on Tue Jun 10 08:29:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3z_62034/06_2025/9k3z_62034.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3z_62034/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3z_62034/06_2025/9k3z_62034.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3z_62034/06_2025/9k3z_62034.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3z_62034/06_2025/9k3z_62034.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3z_62034/06_2025/9k3z_62034.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.050
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.95, per 1000 atoms: 0.76
  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: 2.99
  Conformation dependent library (CDL) restraints added in 987.2 milliseconds
  

  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: 7.33
  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: 4.83

  Time building geometry restraints manager: 3.36 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:             1.220
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     36.590
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.880
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (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
 HIS   0.002   0.001   HIS C  52 
 PHE   0.007   0.001   PHE D  88 
 TYR   0.009   0.001   TYR D  63 
 ARG   0.003   0.000   ARG C  43 

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

*********************** 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  : 0.931 
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: 1.4845
  time to fit residues: 348.3929
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  : 0.842 
-------------------------------------------------------------------------------
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 84 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0670
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.3724

-------------------------------------------------------------------------------
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
E 108 ASN
E 125 GLN
F  75 HIS
F  93 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.070962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.048113 restraints weight = 37292.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 1.94
r_work: 0.2685 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12619  Z= 0.182
  Angle     :  0.580   5.579  18285  Z= 0.355
  Chirality :  0.035   0.152   2097
  Planarity :  0.004   0.032   1296
  Dihedral  : 31.307  88.643   4072
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.30), residues: 728
  helix:  2.74 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.34 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  52 
 PHE   0.007   0.001   PHE D  93 
 TYR   0.011   0.001   TYR G  69 
 ARG   0.006   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04620 (  770)
  hydrogen bonds       : angle       3.03559 ( 1936)
  covalent geometry    : bond        0.00397 (12619)
  covalent geometry    : angle       0.57980 (18285)

*********************** 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
  199 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8061 (pt0) cc_final: 0.7779 (pm20)
REVERT: C   88 LYS cc_start: 0.9378 (mttp) cc_final: 0.9175 (mttp)
REVERT: C  102 ASP cc_start: 0.9012 (t0) cc_final: 0.8742 (t0)
REVERT: C  104 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9025 (mm-30)
REVERT: D  128 GLU cc_start: 0.8589 (tp30) cc_final: 0.8292 (tp30)
REVERT: D  129 LEU cc_start: 0.9528 (tp) cc_final: 0.9322 (tp)
REVERT: E   59 GLU cc_start: 0.8062 (pt0) cc_final: 0.7851 (pm20)
REVERT: E  120 MET cc_start: 0.8719 (mtp) cc_final: 0.8338 (mtp)
REVERT: G   48 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8594 (tpp80)
REVERT: G   88 LYS cc_start: 0.9366 (mtmt) cc_final: 0.9143 (mtmt)
REVERT: H   94 GLU cc_start: 0.9262 (tp30) cc_final: 0.8983 (tp30)
REVERT: H  128 GLU cc_start: 0.8485 (tp30) cc_final: 0.8150 (tp30)
  outliers start: 21
  outliers final: 7
  residues processed: 185
  average time/residue: 1.4249
  time to fit residues: 282.0885
Evaluate side-chains
  162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
D 132 HIS
H  98 GLN
H 132 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.071574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.049394 restraints weight = 37576.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 1.94
r_work: 0.2717 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12619  Z= 0.155
  Angle     :  0.557   6.000  18285  Z= 0.344
  Chirality :  0.034   0.155   2097
  Planarity :  0.004   0.030   1296
  Dihedral  : 31.085  86.618   4069
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.61 (0.30), residues: 728
  helix:  2.97 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.44 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.006   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  770)
  hydrogen bonds       : angle       2.89270 ( 1936)
  covalent geometry    : bond        0.00333 (12619)
  covalent geometry    : angle       0.55676 (18285)

*********************** 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
  195 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.881 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8071 (pt0) cc_final: 0.7850 (pm20)
REVERT: C   48 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8790 (tpp80)
REVERT: C  102 ASP cc_start: 0.9021 (t0) cc_final: 0.8671 (t0)
REVERT: C  104 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8964 (mm-30)
REVERT: D   80 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8934 (mmmm)
REVERT: D   91 ASP cc_start: 0.9388 (t0) cc_final: 0.8966 (t0)
REVERT: D  128 GLU cc_start: 0.8415 (tp30) cc_final: 0.8073 (tp30)
REVERT: D  129 LEU cc_start: 0.9516 (tp) cc_final: 0.9314 (tp)
REVERT: G   46 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8985 (mtpp)
REVERT: G   48 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8559 (tpp80)
REVERT: H   91 ASP cc_start: 0.9418 (t0) cc_final: 0.8941 (t0)
REVERT: H   94 GLU cc_start: 0.9245 (tp30) cc_final: 0.8831 (tp30)
  outliers start: 19
  outliers final: 4
  residues processed: 184
  average time/residue: 1.4310
  time to fit residues: 281.8298
Evaluate side-chains
  157 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   50 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 83 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.071732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.048981 restraints weight = 37457.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 1.95
r_work: 0.2713 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12619  Z= 0.161
  Angle     :  0.561   6.318  18285  Z= 0.344
  Chirality :  0.034   0.157   2097
  Planarity :  0.004   0.030   1296
  Dihedral  : 31.041  84.498   4069
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.81 (0.30), residues: 728
  helix:  3.08 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.62 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.013   0.001   TYR G  69 
 ARG   0.005   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  770)
  hydrogen bonds       : angle       2.82923 ( 1936)
  covalent geometry    : bond        0.00349 (12619)
  covalent geometry    : angle       0.56076 (18285)

*********************** 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
  188 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.836 
Fit side-chains
REVERT: B   93 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8927 (mp10)
REVERT: B   95 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7329 (mmm160)
REVERT: C  102 ASP cc_start: 0.9045 (t0) cc_final: 0.8652 (t0)
REVERT: C  104 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9015 (mm-30)
REVERT: D   91 ASP cc_start: 0.9405 (t0) cc_final: 0.8994 (t0)
REVERT: D   99 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8952 (tp30)
REVERT: F   93 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8923 (mp10)
REVERT: G   48 ARG cc_start: 0.9068 (tpp80) cc_final: 0.8584 (tpp80)
REVERT: G   88 LYS cc_start: 0.9350 (mtmt) cc_final: 0.9129 (mtmt)
REVERT: G  104 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9018 (mm-30)
REVERT: H   91 ASP cc_start: 0.9418 (t0) cc_final: 0.9031 (t0)
REVERT: H   94 GLU cc_start: 0.9234 (tp30) cc_final: 0.8870 (tp30)
REVERT: H  128 GLU cc_start: 0.8320 (tp30) cc_final: 0.8067 (tp30)
  outliers start: 17
  outliers final: 6
  residues processed: 178
  average time/residue: 1.4760
  time to fit residues: 280.6783
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 157
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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   50 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   26 ILE
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue  112 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.069430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.046494 restraints weight = 37538.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.95
r_work: 0.2652 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  12619  Z= 0.205
  Angle     :  0.582   6.619  18285  Z= 0.355
  Chirality :  0.035   0.159   2097
  Planarity :  0.004   0.031   1296
  Dihedral  : 31.329  87.338   4069
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 25.40 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (0.30), residues: 728
  helix:  3.07 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.55 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F  75 
 PHE   0.007   0.001   PHE C  36 
 TYR   0.011   0.001   TYR G  62 
 ARG   0.006   0.000   ARG G  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04646 (  770)
  hydrogen bonds       : angle       2.94204 ( 1936)
  covalent geometry    : bond        0.00461 (12619)
  covalent geometry    : angle       0.58195 (18285)

*********************** 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
  177 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8234 (pm20) cc_final: 0.8019 (pm20)
REVERT: B   79 LYS cc_start: 0.9303 (mttp) cc_final: 0.8938 (mtmt)
REVERT: B   95 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7423 (mmm160)
REVERT: C  102 ASP cc_start: 0.9048 (t0) cc_final: 0.8683 (t0)
REVERT: C  104 GLU cc_start: 0.9261 (mm-30) cc_final: 0.9028 (mm-30)
REVERT: D   91 ASP cc_start: 0.9400 (t0) cc_final: 0.9005 (t0)
REVERT: D   99 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8951 (tp30)
REVERT: F   95 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7456 (mmm160)
REVERT: G   46 LYS cc_start: 0.9287 (mtpp) cc_final: 0.8999 (mtpp)
REVERT: G  104 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9054 (mm-30)
REVERT: H   91 ASP cc_start: 0.9431 (t0) cc_final: 0.9051 (t0)
REVERT: H   94 GLU cc_start: 0.9232 (tp30) cc_final: 0.9021 (tp30)
  outliers start: 20
  outliers final: 7
  residues processed: 168
  average time/residue: 1.5834
  time to fit residues: 283.1665
Evaluate side-chains
  158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 D residue   57 VAL
Chi-restraints excluded: chain D residue  101 SER
Chi-restraints excluded: chain E residue   61 LEU
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 2 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.9386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.068664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.046453 restraints weight = 37608.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 1.93
r_work: 0.2645 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12619  Z= 0.213
  Angle     :  0.591   6.641  18285  Z= 0.359
  Chirality :  0.035   0.152   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 31.337  88.769   4069
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.88 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (0.30), residues: 728
  helix:  3.07 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.55 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.006   0.001   PHE C  36 
 TYR   0.012   0.002   TYR C  62 
 ARG   0.007   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  770)
  hydrogen bonds       : angle       2.87742 ( 1936)
  covalent geometry    : bond        0.00478 (12619)
  covalent geometry    : angle       0.59065 (18285)

*********************** 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
  181 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8326 (pm20) cc_final: 0.8067 (pm20)
REVERT: B   79 LYS cc_start: 0.9320 (mttp) cc_final: 0.8911 (ttmm)
REVERT: B   95 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7372 (mmm160)
REVERT: C  102 ASP cc_start: 0.9061 (t0) cc_final: 0.8703 (t0)
REVERT: C  104 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9040 (mm-30)
REVERT: D   91 ASP cc_start: 0.9388 (t0) cc_final: 0.8994 (t0)
REVERT: D  101 SER cc_start: 0.9686 (m) cc_final: 0.9371 (p)
REVERT: F   95 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7433 (mmm160)
REVERT: G   46 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8936 (mtpp)
REVERT: G   88 LYS cc_start: 0.9471 (mtmt) cc_final: 0.8839 (ptmm)
REVERT: G  104 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9065 (mm-30)
REVERT: H   91 ASP cc_start: 0.9412 (t0) cc_final: 0.9044 (t0)
REVERT: H   94 GLU cc_start: 0.9258 (tp30) cc_final: 0.9025 (tp30)
  outliers start: 23
  outliers final: 9
  residues processed: 171
  average time/residue: 1.5691
  time to fit residues: 285.0289
Evaluate side-chains
  161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain G residue  112 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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
E  68 GLN
H  70 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.069402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.047432 restraints weight = 37575.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 1.96
r_work: 0.2667 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12619  Z= 0.161
  Angle     :  0.586   6.576  18285  Z= 0.355
  Chirality :  0.035   0.154   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 31.335  88.492   4069
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.65 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.74 (0.30), residues: 728
  helix:  3.03 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.60 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.016   0.001   TYR C  62 
 ARG   0.008   0.000   ARG G  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  770)
  hydrogen bonds       : angle       2.82407 ( 1936)
  covalent geometry    : bond        0.00352 (12619)
  covalent geometry    : angle       0.58558 (18285)

*********************** 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
  177 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8269 (pm20) cc_final: 0.8049 (pm20)
REVERT: B   79 LYS cc_start: 0.9330 (mttp) cc_final: 0.8920 (ttmm)
REVERT: B   95 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7322 (mmm160)
REVERT: C  102 ASP cc_start: 0.9066 (t0) cc_final: 0.8732 (t0)
REVERT: C  104 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9018 (mm-30)
REVERT: D   91 ASP cc_start: 0.9371 (t0) cc_final: 0.9008 (t0)
REVERT: D  101 SER cc_start: 0.9686 (m) cc_final: 0.9359 (p)
REVERT: F   95 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7410 (mmm160)
REVERT: G   46 LYS cc_start: 0.9208 (mtpp) cc_final: 0.8916 (mtpp)
REVERT: G   48 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8784 (tpp80)
REVERT: G   88 LYS cc_start: 0.9468 (mtmt) cc_final: 0.8790 (ptmm)
REVERT: H   91 ASP cc_start: 0.9391 (t0) cc_final: 0.9028 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 170
  average time/residue: 1.5187
  time to fit residues: 274.6959
Evaluate side-chains
  165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain G residue  112 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.1184

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.069524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.047321 restraints weight = 37551.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 1.95
r_work: 0.2677 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12619  Z= 0.170
  Angle     :  0.585   6.998  18285  Z= 0.355
  Chirality :  0.034   0.159   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.201  87.002   4069
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.14 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.30), residues: 728
  helix:  3.09 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.66 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B  75 
 PHE   0.006   0.001   PHE F  61 
 TYR   0.015   0.002   TYR C  62 
 ARG   0.009   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  770)
  hydrogen bonds       : angle       2.78635 ( 1936)
  covalent geometry    : bond        0.00375 (12619)
  covalent geometry    : angle       0.58490 (18285)

*********************** 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
  177 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.975 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9330 (mttp) cc_final: 0.8906 (ttmm)
REVERT: B   95 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7349 (mmm160)
REVERT: C   84 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8914 (t0)
REVERT: C  102 ASP cc_start: 0.9049 (t0) cc_final: 0.8720 (t0)
REVERT: C  104 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9017 (mm-30)
REVERT: D   91 ASP cc_start: 0.9381 (t0) cc_final: 0.9022 (t0)
REVERT: D  101 SER cc_start: 0.9696 (m) cc_final: 0.9351 (p)
REVERT: D  128 GLU cc_start: 0.8291 (tp30) cc_final: 0.7779 (mm-30)
REVERT: F   95 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7392 (mmm160)
REVERT: G   46 LYS cc_start: 0.9188 (mtpp) cc_final: 0.8906 (mtpp)
REVERT: G   88 LYS cc_start: 0.9443 (mtmt) cc_final: 0.8838 (ptmt)
REVERT: H   58 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: H   91 ASP cc_start: 0.9383 (t0) cc_final: 0.9038 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 168
  average time/residue: 1.5743
  time to fit residues: 281.3914
Evaluate side-chains
  166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
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   63 GLU
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
Chi-restraints excluded: chain G residue  112 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   chunk 86 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.068660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.046226 restraints weight = 37947.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 1.94
r_work: 0.2644 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  12619  Z= 0.209
  Angle     :  0.607   7.040  18285  Z= 0.366
  Chirality :  0.036   0.164   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 31.372  89.595   4069
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.94 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.71 (0.31), residues: 728
  helix:  2.96 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.70 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 132 
 PHE   0.008   0.001   PHE H  88 
 TYR   0.016   0.002   TYR C  62 
 ARG   0.008   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04587 (  770)
  hydrogen bonds       : angle       2.93283 ( 1936)
  covalent geometry    : bond        0.00472 (12619)
  covalent geometry    : angle       0.60730 (18285)

*********************** 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: 18
    poor density    : 150
  time to evaluate  : 0.934 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9307 (mttp) cc_final: 0.8915 (ttmm)
REVERT: B   95 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7421 (mmm160)
REVERT: C  102 ASP cc_start: 0.9027 (t0) cc_final: 0.8680 (t0)
REVERT: C  104 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9015 (mm-30)
REVERT: D   91 ASP cc_start: 0.9395 (t0) cc_final: 0.9013 (t0)
REVERT: F   95 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7399 (mmm160)
REVERT: G   88 LYS cc_start: 0.9402 (mtmt) cc_final: 0.9156 (mtmt)
REVERT: H   91 ASP cc_start: 0.9413 (t0) cc_final: 0.9054 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 158
  average time/residue: 1.6829
  time to fit residues: 285.1114
Evaluate side-chains
  160 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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   63 GLU
Chi-restraints excluded: chain B residue   95 ARG
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
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   99 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.069320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.046779 restraints weight = 37427.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.95
r_work: 0.2669 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12619  Z= 0.160
  Angle     :  0.601   7.639  18285  Z= 0.363
  Chirality :  0.035   0.162   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 31.362  89.487   4069
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 29.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.31), residues: 728
  helix:  2.91 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.68 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.016   0.002   TYR G  62 
 ARG   0.009   0.000   ARG H 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04332 (  770)
  hydrogen bonds       : angle       2.83999 ( 1936)
  covalent geometry    : bond        0.00349 (12619)
  covalent geometry    : angle       0.60107 (18285)

********************** 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
  169 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.995 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9299 (mttp) cc_final: 0.8914 (ttmm)
REVERT: B   95 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7371 (mmm160)
REVERT: C   46 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9092 (mtpp)
REVERT: C  102 ASP cc_start: 0.9019 (t0) cc_final: 0.8721 (t0)
REVERT: C  104 GLU cc_start: 0.9244 (mm-30) cc_final: 0.9005 (mm-30)
REVERT: D   91 ASP cc_start: 0.9380 (t0) cc_final: 0.9008 (t0)
REVERT: D  128 GLU cc_start: 0.8338 (tp30) cc_final: 0.8039 (tp30)
REVERT: F   95 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7408 (mmm160)
REVERT: G   46 LYS cc_start: 0.9258 (mtpp) cc_final: 0.8928 (mtpp)
REVERT: G   88 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9155 (mtmt)
REVERT: H   91 ASP cc_start: 0.9391 (t0) cc_final: 0.9041 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 161
  average time/residue: 2.0009
  time to fit residues: 342.6649
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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 D residue  101 SER
Chi-restraints excluded: chain E residue   61 LEU
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   50 THR
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   99 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.069467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.046913 restraints weight = 37378.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.95
r_work: 0.2675 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12619  Z= 0.174
  Angle     :  0.597   7.468  18285  Z= 0.360
  Chirality :  0.034   0.159   2097
  Planarity :  0.004   0.038   1296
  Dihedral  : 31.194  88.563   4069
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 29.74 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.76 (0.31), residues: 728
  helix:  2.99 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.72 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 132 
 PHE   0.006   0.001   PHE F  61 
 TYR   0.016   0.002   TYR G  62 
 ARG   0.008   0.000   ARG D 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  770)
  hydrogen bonds       : angle       2.80583 ( 1936)
  covalent geometry    : bond        0.00388 (12619)
  covalent geometry    : angle       0.59705 (18285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9426.77 seconds
wall clock time: 165 minutes 17.26 seconds (9917.26 seconds total)