Starting phenix.real_space_refine
on Thu Sep 18 04:42:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8g_29850/09_2025/8g8g_29850.map"
  }
  resolution = 3.2
  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=   0.004
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     348      5.49       5
     S      17      5.16       5
     C    8089      2.51       5
     N    2711      2.21       5
     O    3393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  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: 14558
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 895
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 915
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 3539
          Classifications: {'DNA': 174}
          Link IDs: {'rna3p': 173}
    Chain: "J"
      Number of atoms: 3595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 3595
          Classifications: {'DNA': 174}
          Link IDs: {'rna3p': 173}
    Chain: "X"
      Number of atoms: 1152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1152
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 3, 'TRANS': 136}
          Chain breaks: 1
  Time building chain proxies: 2.66, per 1000 atoms: 0.18
  Number of scatterers: 14558
  At special positions: 0
  Unit cell: (97.52, 116.6, 189.74, 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      17     16.00
     P     348     15.00
     O    3393      8.00
     N    2711      7.00
     C    8089      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: 1.03
  Conformation dependent library (CDL) restraints added in 317.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 10 sheets defined
      71.5% alpha, 2.6% beta
      157 base pairs and 325 stacking pairs defined.
    Time for finding SS restraints: 2.43
  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
    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 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.335A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.572A  pdb=" N   GLN D  44 " --> pdb=" O   LYS D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 122
    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 131
    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 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.220A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.537A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 122
    Processing helix  chain 'X' and resid 141 through 161
    Processing helix  chain 'X' and resid 163 through 176
    Processing helix  chain 'X' and resid 180 through 189
      removed outlier: 3.554A  pdb=" N   ILE X 184 " --> pdb=" O   SER X 180 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 193 through 211
      Proline residue:  X 202  - end of helix
    Processing helix  chain 'X' and resid 215 through 220
    Processing helix  chain 'X' and resid 238 through 249
    Processing helix  chain 'X' and resid 256 through 268
      removed outlier: 3.681A  pdb=" N   HIS X 262 " --> pdb=" O   GLN X 258 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 270 through 288
      removed outlier: 4.058A  pdb=" N   SER X 288 " --> pdb=" O   LYS X 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.873A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.630A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.964A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.919A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.035A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    493 hydrogen bonds defined for protein.
    1458 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      379 hydrogen bonds
      758 hydrogen bond angles
      0 basepair planarities
      157 basepair parallelities
      325 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 1.36 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: 2787
        1.33 -     1.45: 5064
        1.45 -     1.57: 6948
        1.57 -     1.69: 694
        1.69 -     1.81: 28
  Bond restraints: 15521
  Sorted by residual:
  bond pdb=" C   LEU G 116 "
       pdb=" N   PRO G 117 "
    ideal  model  delta    sigma   weight residual
    1.332  1.213  0.119 1.34e-02 5.57e+03 7.87e+01
  bond pdb=" C   LEU F  22 "
       pdb=" N   ARG F  23 "
    ideal  model  delta    sigma   weight residual
    1.330  1.384 -0.054 1.22e-02 6.72e+03 1.98e+01
  bond pdb=" N   ASN B  25 "
       pdb=" CA  ASN B  25 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.35e+00
  bond pdb=" N   ILE B  26 "
       pdb=" CA  ILE B  26 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.24e-02 6.50e+03 6.55e+00
  bond pdb=" C   ARG A  40 "
       pdb=" N   TYR A  41 "
    ideal  model  delta    sigma   weight residual
    1.329  1.356 -0.027 1.43e-02 4.89e+03 3.66e+00
  ... (remaining 15516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 22312
        2.38 -     4.76: 108
        4.76 -     7.14: 12
        7.14 -     9.52: 2
        9.52 -    11.90: 1
  Bond angle restraints: 22435
  Sorted by residual:
  angle pdb=" CB  MET X 197 "
        pdb=" CG  MET X 197 "
        pdb=" SD  MET X 197 "
      ideal   model   delta    sigma   weight residual
     112.70  124.60  -11.90 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" CA  GLU X 238 "
        pdb=" CB  GLU X 238 "
        pdb=" CG  GLU X 238 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" O3'  DA I  74 "
        pdb=" C3'  DA I  74 "
        pdb=" C2'  DA I  74 "
      ideal   model   delta    sigma   weight residual
     111.50  116.28   -4.78 1.50e+00 4.44e-01 1.02e+01
  angle pdb=" CB  LYS A  37 "
        pdb=" CG  LYS A  37 "
        pdb=" CD  LYS A  37 "
      ideal   model   delta    sigma   weight residual
     111.30  117.84   -6.54 2.30e+00 1.89e-01 8.09e+00
  angle pdb=" C3'  DT J -88 "
        pdb=" C2'  DT J -88 "
        pdb=" C1'  DT J -88 "
      ideal   model   delta    sigma   weight residual
     101.60   97.56    4.04 1.50e+00 4.44e-01 7.25e+00
  ... (remaining 22430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 6918
       35.91 -    71.82: 1652
       71.82 -   107.73: 18
      107.73 -   143.64: 2
      143.64 -   179.55: 1
  Dihedral angle restraints: 8591
    sinusoidal: 5887
      harmonic: 2704
  Sorted by residual:
  dihedral pdb=" C4'  DC I  20 "
           pdb=" C3'  DC I  20 "
           pdb=" O3'  DC I  20 "
           pdb=" P    DT I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.45  179.55     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J -93 "
           pdb=" C3'  DG J -93 "
           pdb=" O3'  DG J -93 "
           pdb=" P    DG J -92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.86  138.14     1      3.50e+01 8.16e-04 1.37e+01
  dihedral pdb=" C4'  DA I  52 "
           pdb=" C3'  DA I  52 "
           pdb=" O3'  DA I  52 "
           pdb=" P    DA I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.27  135.73     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 8588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 2008
       0.038 -    0.076: 454
       0.076 -    0.114: 74
       0.114 -    0.152: 12
       0.152 -    0.190: 2
  Chirality restraints: 2550
  Sorted by residual:
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.03e-01
  chirality pdb=" CG  LEU X 190 "
            pdb=" CB  LEU X 190 "
            pdb=" CD1 LEU X 190 "
            pdb=" CD2 LEU X 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.83e-01
  chirality pdb=" CA  LEU X 267 "
            pdb=" N   LEU X 267 "
            pdb=" C   LEU X 267 "
            pdb=" CB  LEU X 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 2547 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  22 "    0.022 2.00e-02 2.50e+03   4.48e-02 2.00e+01
        pdb=" C   LEU F  22 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LEU F  22 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ARG F  23 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.033 5.00e-02 4.00e+02   4.98e-02 3.98e+00
        pdb=" N   PRO E  43 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  40 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" C   ARG A  40 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ARG A  40 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR A  41 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.28: 7
        2.28 -     2.93: 5418
        2.93 -     3.59: 21629
        3.59 -     4.24: 41392
        4.24 -     4.90: 59753
  Nonbonded interactions: 128199
  Sorted by model distance:
  nonbonded pdb=" O   SER G 123 "
            pdb=" OP1  DG J -75 "
     model   vdw
     1.622 3.040
  nonbonded pdb=" CD  LYS G 124 "
            pdb=" O3'  DA J -76 "
     model   vdw
     1.932 3.440
  nonbonded pdb=" C   SER G 123 "
            pdb=" OP1  DG J -75 "
     model   vdw
     2.057 3.270
  nonbonded pdb=" NH1 ARG A  26 "
            pdb=" OP1  DA J   2 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.238 3.120
  ... (remaining 128194 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 28 through 122)
  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=0.99
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:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     15.000
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4882
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.119  15521  Z= 0.230
  Angle     :  0.593  11.899  22435  Z= 0.354
  Chirality :  0.033   0.190   2550
  Planarity :  0.004   0.050   1630
  Dihedral  : 27.409 179.553   6839
  Min Nonbonded Distance : 1.622

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 14.27 %
    Favored  : 85.10 %
  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: -0.50 (0.25), residues: 911
  helix:  0.14 (0.19), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.29 (0.33), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  42 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.011   0.001   PHE X 187 
 TRP   0.022   0.003   TRP X 277 
 HIS   0.004   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (15521)
  covalent geometry    : angle       0.59320 (22435)
  hydrogen bonds       : bond        0.20972 (  872)
  hydrogen bonds       : angle       6.94673 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 271
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.5202 (mt) cc_final: 0.4916 (mt)
REVERT: F   19 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7445 (ptp-170)
REVERT: F   20 LYS cc_start: 0.7435 (tppt) cc_final: 0.7206 (tppt)
  outliers start: 5
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1445
  time to fit residues: 54.6566
Evaluate side-chains
  135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
C 110 ASN
E  55 GLN
E  76 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
H  81 ASN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.077383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.051164 restraints weight = 95732.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 3.59
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085  15521  Z= 0.284
  Angle     :  0.791   8.271  22435  Z= 0.457
  Chirality :  0.042   0.169   2550
  Planarity :  0.006   0.053   1630
  Dihedral  : 31.036 175.606   4949
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.75 %
    Favored  : 76.18 %
  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:  0.87 (0.26), residues: 911
  helix:  1.31 (0.19), residues: 661
  sheet:  None (None), residues: 0
  loop : -1.38 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  20 
 TYR   0.029   0.003   TYR A  54 
 PHE   0.016   0.002   PHE H  62 
 TRP   0.006   0.002   TRP X 277 
 HIS   0.008   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (15521)
  covalent geometry    : angle       0.79085 (22435)
  hydrogen bonds       : bond        0.06083 (  872)
  hydrogen bonds       : angle       3.67991 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: B   34 ILE cc_start: 0.8346 (mt) cc_final: 0.8119 (mp)
REVERT: B   59 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7286 (mtpp)
REVERT: B   88 TYR cc_start: 0.8183 (m-10) cc_final: 0.7825 (m-80)
REVERT: C   36 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8474 (mmtm)
REVERT: E   90 MET cc_start: 0.8873 (mmm) cc_final: 0.8644 (mmt)
REVERT: F   19 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7467 (ptp-170)
REVERT: F   63 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8544 (mt-10)
REVERT: F   96 THR cc_start: 0.9379 (m) cc_final: 0.9157 (p)
REVERT: G   91 GLU cc_start: 0.7859 (pm20) cc_final: 0.7081 (pm20)
  outliers start: 32
  outliers final: 13
  residues processed: 161
  average time/residue: 0.1272
  time to fit residues: 29.7504
Evaluate side-chains
  120 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain X residue  158 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0170
   chunk 117 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.6026

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
X 181 GLN
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.069764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.042706 restraints weight = 95891.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 4.05
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.8285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109  15521  Z= 0.231
  Angle     :  0.729   8.169  22435  Z= 0.424
  Chirality :  0.039   0.203   2550
  Planarity :  0.006   0.055   1630
  Dihedral  : 30.737 178.648   4949
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.55 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.32 (0.27), residues: 911
  helix:  1.66 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.30 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  20 
 TYR   0.016   0.002   TYR H  37 
 PHE   0.023   0.002   PHE E  78 
 TRP   0.008   0.001   TRP X 277 
 HIS   0.008   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 (15521)
  covalent geometry    : angle       0.72914 (22435)
  hydrogen bonds       : bond        0.05775 (  872)
  hydrogen bonds       : angle       3.41871 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8608 (tt0) cc_final: 0.8349 (tt0)
REVERT: B   59 LYS cc_start: 0.8377 (ptmt) cc_final: 0.8177 (mtpt)
REVERT: B   63 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8043 (mp0)
REVERT: B   88 TYR cc_start: 0.8736 (m-10) cc_final: 0.8389 (m-10)
REVERT: C   90 ASP cc_start: 0.8556 (t0) cc_final: 0.8264 (t0)
REVERT: D   31 LYS cc_start: 0.8879 (tppt) cc_final: 0.8638 (ptpp)
REVERT: E   56 LYS cc_start: 0.9268 (ptmm) cc_final: 0.9042 (ttpp)
REVERT: E   59 GLU cc_start: 0.8049 (pm20) cc_final: 0.7736 (pm20)
REVERT: E   77 ASP cc_start: 0.9067 (m-30) cc_final: 0.8777 (m-30)
REVERT: E  120 MET cc_start: 0.7531 (mmt) cc_final: 0.6439 (mmm)
REVERT: E  123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8043 (m-30)
REVERT: F   19 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7198 (ptp-170)
REVERT: F   24 ASP cc_start: 0.8662 (t0) cc_final: 0.8380 (t0)
REVERT: F   63 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8567 (mt-10)
REVERT: G   61 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8644 (tp30)
REVERT: G   64 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8044 (tm-30)
  outliers start: 16
  outliers final: 4
  residues processed: 145
  average time/residue: 0.1316
  time to fit residues: 27.4217
Evaluate side-chains
  106 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 91 optimal weight:   30.0000
   chunk 82 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 86 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:   30.0000
   chunk 95 optimal weight:    7.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.063530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.035848 restraints weight = 93900.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.56
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          1.0590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  15521  Z= 0.266
  Angle     :  0.708   8.485  22435  Z= 0.414
  Chirality :  0.039   0.162   2550
  Planarity :  0.005   0.051   1630
  Dihedral  : 31.169 176.791   4949
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.66 %
    Favored  : 76.18 %
  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:  1.46 (0.27), residues: 911
  helix:  1.82 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.42 (0.34), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  96 
 TYR   0.010   0.001   TYR C  57 
 PHE   0.022   0.002   PHE E  78 
 TRP   0.008   0.002   TRP X 277 
 HIS   0.006   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 (15521)
  covalent geometry    : angle       0.70815 (22435)
  hydrogen bonds       : bond        0.05476 (  872)
  hydrogen bonds       : angle       3.45898 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8876 (mm-30)
REVERT: B   59 LYS cc_start: 0.8563 (ptmt) cc_final: 0.8242 (mtpp)
REVERT: B   63 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7928 (mp0)
REVERT: B   84 MET cc_start: 0.9194 (mmm) cc_final: 0.8823 (mmm)
REVERT: B   88 TYR cc_start: 0.8880 (m-10) cc_final: 0.8537 (m-10)
REVERT: C   90 ASP cc_start: 0.8759 (t0) cc_final: 0.8413 (t0)
REVERT: D   82 LYS cc_start: 0.9622 (mmtp) cc_final: 0.9411 (mmtm)
REVERT: E   59 GLU cc_start: 0.8143 (pm20) cc_final: 0.7853 (pm20)
REVERT: E  120 MET cc_start: 0.7943 (mmt) cc_final: 0.6901 (mmm)
REVERT: E  123 ASP cc_start: 0.8938 (m-30) cc_final: 0.8135 (m-30)
REVERT: F   63 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8595 (mt-10)
REVERT: F   79 LYS cc_start: 0.9030 (mttp) cc_final: 0.8587 (mtmm)
REVERT: G   64 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: H   48 ASP cc_start: 0.9403 (p0) cc_final: 0.9198 (p0)
REVERT: H   73 GLU cc_start: 0.9112 (tp30) cc_final: 0.8876 (mm-30)
  outliers start: 17
  outliers final: 8
  residues processed: 138
  average time/residue: 0.1340
  time to fit residues: 26.3912
Evaluate side-chains
  110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.063110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.036320 restraints weight = 91949.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.72
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          1.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15521  Z= 0.203
  Angle     :  0.626   7.938  22435  Z= 0.373
  Chirality :  0.035   0.135   2550
  Planarity :  0.004   0.044   1630
  Dihedral  : 30.933 176.805   4949
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.53 %
    Favored  : 76.43 %
  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:  1.89 (0.28), residues: 911
  helix:  2.13 (0.20), residues: 667
  sheet:  None (None), residues: 0
  loop : -1.31 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  76 
 TYR   0.010   0.001   TYR H  37 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.007   0.002   TRP X 277 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (15521)
  covalent geometry    : angle       0.62646 (22435)
  hydrogen bonds       : bond        0.04230 (  872)
  hydrogen bonds       : angle       3.14533 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8822 (mm-30)
REVERT: B   59 LYS cc_start: 0.8694 (ptmt) cc_final: 0.8341 (mtpp)
REVERT: B   63 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8036 (mp0)
REVERT: B   74 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8175 (mp0)
REVERT: B   88 TYR cc_start: 0.8941 (m-10) cc_final: 0.8428 (m-10)
REVERT: C   90 ASP cc_start: 0.8643 (t0) cc_final: 0.8286 (t0)
REVERT: E   59 GLU cc_start: 0.8180 (pm20) cc_final: 0.7939 (pm20)
REVERT: E  120 MET cc_start: 0.7930 (mmt) cc_final: 0.6585 (mtt)
REVERT: E  123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8251 (m-30)
REVERT: F   63 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8607 (mt-10)
REVERT: F   79 LYS cc_start: 0.9081 (mttp) cc_final: 0.8595 (mtmm)
REVERT: G   41 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8220 (tp30)
REVERT: G   64 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: G   92 GLU cc_start: 0.8629 (mp0) cc_final: 0.8259 (mp0)
REVERT: H   73 GLU cc_start: 0.9002 (tp30) cc_final: 0.8577 (mm-30)
REVERT: X  140 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6719 (tmtt)
  outliers start: 16
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1204
  time to fit residues: 22.0310
Evaluate side-chains
  108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain X residue  140 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 122 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS
F  93 GLN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 283 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.060534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.033671 restraints weight = 94033.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.79
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          1.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  15521  Z= 0.291
  Angle     :  0.683   8.765  22435  Z= 0.401
  Chirality :  0.039   0.147   2550
  Planarity :  0.005   0.046   1630
  Dihedral  : 31.484 176.245   4949
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.29 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.81 (0.28), residues: 911
  helix:  2.11 (0.20), residues: 663
  sheet:  None (None), residues: 0
  loop : -1.39 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 116 
 TYR   0.010   0.002   TYR H  34 
 PHE   0.013   0.002   PHE X 187 
 TRP   0.008   0.002   TRP X 277 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (15521)
  covalent geometry    : angle       0.68308 (22435)
  hydrogen bonds       : bond        0.05928 (  872)
  hydrogen bonds       : angle       3.44645 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9065 (tt0) cc_final: 0.8849 (tt0)
REVERT: B   63 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: B   74 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7985 (mt-10)
REVERT: B   84 MET cc_start: 0.9256 (mmm) cc_final: 0.9025 (mmm)
REVERT: B   88 TYR cc_start: 0.9059 (m-10) cc_final: 0.8569 (m-10)
REVERT: C   38 ASN cc_start: 0.7943 (t0) cc_final: 0.7737 (t0)
REVERT: C   90 ASP cc_start: 0.8822 (t0) cc_final: 0.8571 (t0)
REVERT: D   31 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8626 (ptpp)
REVERT: E   59 GLU cc_start: 0.8330 (pm20) cc_final: 0.8113 (pm20)
REVERT: E  120 MET cc_start: 0.8147 (mmt) cc_final: 0.7095 (mmm)
REVERT: E  123 ASP cc_start: 0.8902 (m-30) cc_final: 0.8204 (m-30)
REVERT: F   79 LYS cc_start: 0.9105 (mttp) cc_final: 0.8667 (mtmm)
REVERT: G   41 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8091 (tp30)
REVERT: G   64 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: G   92 GLU cc_start: 0.8659 (mp0) cc_final: 0.8297 (mp0)
REVERT: H   68 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8448 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1522
  time to fit residues: 26.0627
Evaluate side-chains
  109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 122 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 114 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
F  75 HIS
H  81 ASN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.062415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.034997 restraints weight = 89037.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.56
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          1.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15521  Z= 0.155
  Angle     :  0.609   8.380  22435  Z= 0.360
  Chirality :  0.034   0.131   2550
  Planarity :  0.004   0.045   1630
  Dihedral  : 30.987 175.292   4949
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 22.42 %
    Favored  : 76.31 %
  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:  2.12 (0.28), residues: 911
  helix:  2.32 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.24 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  67 
 TYR   0.011   0.001   TYR H  37 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.011   0.002   TRP X 207 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15521)
  covalent geometry    : angle       0.60894 (22435)
  hydrogen bonds       : bond        0.03648 (  872)
  hydrogen bonds       : angle       3.00130 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8913 (tt0) cc_final: 0.8691 (tt0)
REVERT: A   94 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8756 (mm-30)
REVERT: B   27 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8954 (mm110)
REVERT: B   59 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8385 (tttm)
REVERT: B   63 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8055 (mp0)
REVERT: B   88 TYR cc_start: 0.9004 (m-10) cc_final: 0.8499 (m-10)
REVERT: C   92 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8502 (mt-10)
REVERT: D   31 LYS cc_start: 0.8917 (ptpp) cc_final: 0.8695 (ptpp)
REVERT: E  120 MET cc_start: 0.7962 (mmt) cc_final: 0.6624 (mtt)
REVERT: E  123 ASP cc_start: 0.8784 (m-30) cc_final: 0.8256 (m-30)
REVERT: F   59 LYS cc_start: 0.9289 (ttmm) cc_final: 0.9025 (ttpp)
REVERT: F   63 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: G   41 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7986 (tp30)
REVERT: G   64 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: G   92 GLU cc_start: 0.8692 (mp0) cc_final: 0.8282 (mp0)
REVERT: H   54 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8925 (mmmm)
REVERT: H   73 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8432 (mm-30)
REVERT: H   90 GLU cc_start: 0.9053 (mp0) cc_final: 0.8298 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 129
  average time/residue: 0.1361
  time to fit residues: 25.1342
Evaluate side-chains
  113 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    8.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.062218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.034873 restraints weight = 89717.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.51
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          1.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15521  Z= 0.168
  Angle     :  0.620  10.088  22435  Z= 0.364
  Chirality :  0.034   0.233   2550
  Planarity :  0.004   0.043   1630
  Dihedral  : 30.888 175.072   4949
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.44 %
    Favored  : 75.16 %
  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:  2.16 (0.28), residues: 911
  helix:  2.34 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.19 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.009   0.001   TYR H  37 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.008   0.002   TRP X 207 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (15521)
  covalent geometry    : angle       0.62037 (22435)
  hydrogen bonds       : bond        0.03728 (  872)
  hydrogen bonds       : angle       3.03900 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8919 (tt0) cc_final: 0.8688 (tt0)
REVERT: A   93 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8954 (tp40)
REVERT: A   94 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8699 (mm-30)
REVERT: B   63 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8060 (mp0)
REVERT: B   74 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8006 (mp0)
REVERT: B   88 TYR cc_start: 0.9024 (m-10) cc_final: 0.8469 (m-10)
REVERT: D   31 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8697 (ptpp)
REVERT: E  120 MET cc_start: 0.7985 (mmt) cc_final: 0.6638 (mtt)
REVERT: E  123 ASP cc_start: 0.8761 (m-30) cc_final: 0.8258 (m-30)
REVERT: F   79 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8839 (mtmm)
REVERT: G   41 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7959 (tp30)
REVERT: G   64 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7671 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 121
  average time/residue: 0.1401
  time to fit residues: 24.3575
Evaluate side-chains
  110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 121 optimal weight:    8.9990
   chunk 58 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   overall best weight:    4.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.060024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.033422 restraints weight = 93712.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.67
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          1.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  15521  Z= 0.274
  Angle     :  0.675  10.241  22435  Z= 0.394
  Chirality :  0.037   0.229   2550
  Planarity :  0.005   0.043   1630
  Dihedral  : 31.276 175.511   4949
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.44 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.28), residues: 911
  helix:  2.17 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.26 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A  69 
 TYR   0.010   0.001   TYR C  57 
 PHE   0.035   0.002   PHE A  67 
 TRP   0.007   0.002   TRP X 277 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 (15521)
  covalent geometry    : angle       0.67482 (22435)
  hydrogen bonds       : bond        0.05560 (  872)
  hydrogen bonds       : angle       3.32473 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9535 (mtmm) cc_final: 0.9277 (mtpp)
REVERT: A   93 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9143 (tp40)
REVERT: B   27 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (mm110)
REVERT: B   59 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8853 (ttmm)
REVERT: B   63 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8095 (mt-10)
REVERT: B   74 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7809 (mp0)
REVERT: B   88 TYR cc_start: 0.9058 (m-10) cc_final: 0.8534 (m-10)
REVERT: D   31 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8710 (ptpp)
REVERT: E  120 MET cc_start: 0.8190 (mmt) cc_final: 0.7153 (mmm)
REVERT: E  123 ASP cc_start: 0.8798 (m-30) cc_final: 0.8178 (m-30)
REVERT: F   63 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8517 (mt-10)
REVERT: G   41 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8136 (tp30)
REVERT: G   64 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: G   92 GLU cc_start: 0.8945 (mp0) cc_final: 0.8343 (mp0)
REVERT: G  111 ILE cc_start: 0.9401 (mp) cc_final: 0.9163 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1378
  time to fit residues: 23.2803
Evaluate side-chains
  110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain X residue  169 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0270
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    3.2046

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.060457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.033688 restraints weight = 90814.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.62
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          1.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15521  Z= 0.215
  Angle     :  0.641   9.618  22435  Z= 0.376
  Chirality :  0.035   0.217   2550
  Planarity :  0.004   0.048   1630
  Dihedral  : 31.080 175.020   4949
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 24.20 %
    Favored  : 74.90 %
  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:  1.98 (0.28), residues: 911
  helix:  2.16 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.17 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  40 
 TYR   0.017   0.001   TYR B  88 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.007   0.002   TRP X 207 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (15521)
  covalent geometry    : angle       0.64123 (22435)
  hydrogen bonds       : bond        0.04116 (  872)
  hydrogen bonds       : angle       3.14915 ( 2216)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: B   74 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7900 (mp0)
REVERT: D   31 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8731 (ptpp)
REVERT: D  102 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8184 (tp30)
REVERT: E  120 MET cc_start: 0.8097 (mmt) cc_final: 0.6749 (mtt)
REVERT: E  123 ASP cc_start: 0.8747 (m-30) cc_final: 0.8175 (m-30)
REVERT: F   63 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8538 (mt-10)
REVERT: G   41 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8101 (tp30)
REVERT: G   64 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: H   90 GLU cc_start: 0.9027 (mp0) cc_final: 0.8199 (mp0)
  outliers start: 7
  outliers final: 5
  residues processed: 111
  average time/residue: 0.1330
  time to fit residues: 21.4431
Evaluate side-chains
  107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0870
   chunk 84 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    5.2166

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.058915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.031874 restraints weight = 94040.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 3.36
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          1.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081  15521  Z= 0.311
  Angle     :  0.690  10.769  22435  Z= 0.402
  Chirality :  0.039   0.203   2550
  Planarity :  0.005   0.043   1630
  Dihedral  : 31.348 175.150   4949
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 23.95 %
    Favored  : 75.03 %
  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:  1.79 (0.28), residues: 911
  helix:  2.03 (0.20), residues: 667
  sheet:  None (None), residues: 0
  loop : -1.24 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  69 
 TYR   0.016   0.002   TYR D  80 
 PHE   0.029   0.002   PHE A  67 
 TRP   0.007   0.002   TRP X 207 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (15521)
  covalent geometry    : angle       0.69038 (22435)
  hydrogen bonds       : bond        0.06106 (  872)
  hydrogen bonds       : angle       3.41966 ( 2216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3399.43 seconds
wall clock time: 58 minutes 59.13 seconds (3539.13 seconds total)