Starting phenix.real_space_refine
on Fri Feb 14 11:42:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubb_42081/02_2025/8ubb_42081.cif"
  }
  resolution = 3.23
  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=   0.030
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     148      5.49       5
     S      36      5.16       5
     C    6052      2.51       5
     N    1862      2.21       5
     O    2251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10349
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2690
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 12, 'TRANS': 315}
    Chain: "B"
      Number of atoms: 976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 976
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "D"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 868
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 4, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 876
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "F"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "G"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 289
          Classifications: {'RNA': 13}
          Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 12}
    Chain: "H"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 269
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 12}
    Chain: "I"
      Number of atoms: 2605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2605
          Classifications: {'RNA': 122}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 23, 'rna3p': 98}
          Chain breaks: 2
  Time building chain proxies: 5.09, per 1000 atoms: 0.49
  Number of scatterers: 10349
  At special positions: 0
  Unit cell: (80, 99, 129, 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      36     16.00
     P     148     15.00
     O    2251      8.00
     N    1862      7.00
     C    6052      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: 2.54
  Conformation dependent library (CDL) restraints added in 915.7 milliseconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1672

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 1 sheets defined
      77.1% alpha, 1.9% beta
      38 base pairs and 90 stacking pairs defined.
    Time for finding SS restraints: 4.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 13
    Processing helix  chain 'A' and resid 14 through 27
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.867A  pdb=" N   GLU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 54
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 3.783A  pdb=" N   ILE A  97 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 128
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 183 through 203
      removed outlier: 4.043A  pdb=" N   VAL A 197 " --> pdb=" O   TYR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 207
      removed outlier: 4.397A  pdb=" N   GLN A 207 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 207'
    Processing helix  chain 'A' and resid 223 through 241
    Processing helix  chain 'A' and resid 259 through 263
      removed outlier: 4.530A  pdb=" N   GLY A 262 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 289
    Processing helix  chain 'A' and resid 294 through 309
      removed outlier: 3.893A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   TRP A 309 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'B' and resid 10 through 32
      removed outlier: 3.555A  pdb=" N   ARG B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      Proline residue:  B  29  - end of helix
    Processing helix  chain 'B' and resid 39 through 50
    Processing helix  chain 'B' and resid 51 through 62
    Processing helix  chain 'B' and resid 64 through 88
    Processing helix  chain 'B' and resid 95 through 122
    Processing helix  chain 'C' and resid 12 through 34
      removed outlier: 3.634A  pdb=" N   ARG C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 38 through 50
    Processing helix  chain 'C' and resid 51 through 63
    Processing helix  chain 'C' and resid 64 through 88
    Processing helix  chain 'C' and resid 95 through 121
    Processing helix  chain 'D' and resid 14 through 34
      Proline residue:  D  29  - end of helix
    Processing helix  chain 'D' and resid 35 through 37
      No H-bonds generated for 'chain 'D' and resid 35 through 37'
    Processing helix  chain 'D' and resid 38 through 62
      removed outlier: 3.756A  pdb=" N   VAL D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU D  54 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 86
    Processing helix  chain 'D' and resid 95 through 121
    Processing helix  chain 'E' and resid 13 through 32
      removed outlier: 3.637A  pdb=" N   ARG E  22 " --> pdb=" O   GLU E  18 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      Proline residue:  E  29  - end of helix
    Processing helix  chain 'E' and resid 38 through 62
      removed outlier: 4.083A  pdb=" N   GLY E  51 " --> pdb=" O   LYS E  47 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL E  53 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLU E  54 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 86
      removed outlier: 3.547A  pdb=" N   ASP E  72 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 121
    Processing helix  chain 'F' and resid 14 through 34
      removed outlier: 4.376A  pdb=" N   ARG F  22 " --> pdb=" O   GLU F  18 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      Proline residue:  F  29  - end of helix
      removed outlier: 3.534A  pdb=" N   ILE F  34 " --> pdb=" O   ILE F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 38 through 50
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 64 through 87
    Processing helix  chain 'F' and resid 88 through 93
      Proline residue:  F  91  - end of helix
      No H-bonds generated for 'chain 'F' and resid 88 through 93'
    Processing helix  chain 'F' and resid 95 through 122
      removed outlier: 4.211A  pdb=" N   LEU F 105 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213
      removed outlier: 3.844A  pdb=" N   HIS A 133 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   HIS A 248 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)

    497 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      92 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      90 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 2.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 1685
        1.33 -     1.45: 3592
        1.45 -     1.57: 5249
        1.57 -     1.69: 294
        1.69 -     1.81: 61
  Bond restraints: 10881
  Sorted by residual:
  bond pdb=" CB  ARG B 122 "
       pdb=" CG  ARG B 122 "
    ideal  model  delta    sigma   weight residual
    1.520  1.412  0.108 3.00e-02 1.11e+03 1.29e+01
  bond pdb=" CG1 ILE C  24 "
       pdb=" CD1 ILE C  24 "
    ideal  model  delta    sigma   weight residual
    1.513  1.374  0.139 3.90e-02 6.57e+02 1.26e+01
  bond pdb=" CG1 ILE F  24 "
       pdb=" CD1 ILE F  24 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.21e+01
  bond pdb=" CG1 ILE D  88 "
       pdb=" CD1 ILE D  88 "
    ideal  model  delta    sigma   weight residual
    1.513  1.379  0.134 3.90e-02 6.57e+02 1.18e+01
  bond pdb=" CB  PRO C  91 "
       pdb=" CG  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.492  1.664 -0.172 5.00e-02 4.00e+02 1.18e+01
  ... (remaining 10876 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 14711
        2.60 -     5.20: 592
        5.20 -     7.80: 99
        7.80 -    10.39: 18
       10.39 -    12.99: 4
  Bond angle restraints: 15424
  Sorted by residual:
  angle pdb=" C3'   C I 104 "
        pdb=" O3'   C I 104 "
        pdb=" P     G I 105 "
      ideal   model   delta    sigma   weight residual
     120.20  110.38    9.82 1.50e+00 4.44e-01 4.28e+01
  angle pdb=" N   GLN E  32 "
        pdb=" CA  GLN E  32 "
        pdb=" C   GLN E  32 "
      ideal   model   delta    sigma   weight residual
     113.38  105.47    7.91 1.23e+00 6.61e-01 4.14e+01
  angle pdb=" C   ALA A 153 "
        pdb=" N   MET A 154 "
        pdb=" CA  MET A 154 "
      ideal   model   delta    sigma   weight residual
     120.58  131.13  -10.55 1.71e+00 3.42e-01 3.81e+01
  angle pdb=" C3'   U I   3 "
        pdb=" O3'   U I   3 "
        pdb=" P     G I   4 "
      ideal   model   delta    sigma   weight residual
     120.20  111.15    9.05 1.50e+00 4.44e-01 3.64e+01
  angle pdb=" C3'   A I 119 "
        pdb=" O3'   A I 119 "
        pdb=" P     U I 120 "
      ideal   model   delta    sigma   weight residual
     120.20  111.28    8.92 1.50e+00 4.44e-01 3.54e+01
  ... (remaining 15419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.55: 5887
       35.55 -    71.10: 771
       71.10 -   106.65: 78
      106.65 -   142.20: 4
      142.20 -   177.75: 5
  Dihedral angle restraints: 6745
    sinusoidal: 4152
      harmonic: 2593
  Sorted by residual:
  dihedral pdb=" O4'   U I  94 "
           pdb=" C1'   U I  94 "
           pdb=" N1    U I  94 "
           pdb=" C2    U I  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.57 -174.57     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   C I  82 "
           pdb=" C1'   C I  82 "
           pdb=" N1    C I  82 "
           pdb=" C2    C I  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   76.28  155.72     1      1.70e+01 3.46e-03 6.35e+01
  dihedral pdb=" C5'   C I  20 "
           pdb=" C4'   C I  20 "
           pdb=" C3'   C I  20 "
           pdb=" O3'   C I  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  108.63   38.37     1      8.00e+00 1.56e-02 3.24e+01
  ... (remaining 6742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1718
       0.113 -    0.225: 95
       0.225 -    0.338: 13
       0.338 -    0.450: 4
       0.450 -    0.563: 2
  Chirality restraints: 1832
  Sorted by residual:
  chirality pdb=" P     U I   3 "
            pdb=" OP1   U I   3 "
            pdb=" OP2   U I   3 "
            pdb=" O5'   U I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.93e+00
  chirality pdb=" P     A I  81 "
            pdb=" OP1   A I  81 "
            pdb=" OP2   A I  81 "
            pdb=" O5'   A I  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.22e+00
  chirality pdb=" P     U I 120 "
            pdb=" OP1   U I 120 "
            pdb=" OP2   U I 120 "
            pdb=" O5'   U I 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.85   -0.44 2.00e-01 2.50e+01 4.91e+00
  ... (remaining 1829 not shown)

  Planarity restraints: 1399
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  90 "   -0.087 5.00e-02 4.00e+02   1.33e-01 2.82e+01
        pdb=" N   PRO C  91 "    0.230 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  70 "   -0.064 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO A  71 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 231 "   -0.038 2.00e-02 2.50e+03   2.59e-02 1.18e+01
        pdb=" CG  PHE A 231 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 231 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 231 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 231 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 231 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 231 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1396 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1413
        2.74 -     3.28: 11235
        3.28 -     3.82: 23299
        3.82 -     4.36: 28718
        4.36 -     4.90: 40236
  Nonbonded interactions: 104901
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F  26 "
            pdb=" OG1 THR F 101 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" O   LEU A 242 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NE2 GLN E  98 "
            pdb=" O3'   C I  17 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   ARG A  31 "
            pdb=" OH  TYR B  11 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" NE2 HIS A 202 "
            pdb=" O2'   G I 129 "
     model   vdw
     2.260 3.120
  ... (remaining 104896 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 'B' and resid 13 through 121)
  selection = (chain 'C' and resid 13 through 121)
  selection = chain 'D'
  selection = (chain 'E' and resid 13 through 121)
  selection = (chain 'F' and resid 13 through 121)
}

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:             13.050
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     25.470
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
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      :  0.010   0.172  10881  Z= 0.692
  Angle     :  1.206  12.992  15424  Z= 0.653
  Chirality :  0.064   0.563   1832
  Planarity :  0.010   0.133   1399
  Dihedral  : 25.815 177.753   5073
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 41.97
  Ramachandran Plot:
    Outliers :  3.64 %
    Allowed  : 10.69 %
    Favored  : 85.67 %
  Rotamer:
    Outliers : 20.00 %
    Allowed  : 14.23 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.12 %
  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: -4.10 (0.24), residues: 879
  helix: -2.03 (0.17), residues: 643
  sheet: -3.81 (1.05), residues: 26
  loop : -4.23 (0.36), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP D  81 
 HIS   0.015   0.003   HIS E  38 
 PHE   0.054   0.006   PHE A 231 
 TYR   0.026   0.004   TYR A  41 
 ARG   0.014   0.001   ARG E  42 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 149
    poor density    : 265
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6612 (ppp)
REVERT: A    3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6719 (mttm)
REVERT: A   33 TRP cc_start: 0.7820 (t-100) cc_final: 0.7283 (t60)
REVERT: A   37 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8540 (tt0)
REVERT: A   52 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tt0)
REVERT: A   59 GLU cc_start: 0.8373 (mp0) cc_final: 0.8119 (pt0)
REVERT: A   74 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5073 (ptt180)
REVERT: A  109 CYS cc_start: 0.8194 (m) cc_final: 0.7899 (t)
REVERT: A  123 GLN cc_start: 0.7862 (tt0) cc_final: 0.7647 (tt0)
REVERT: A  130 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (mmm160)
REVERT: A  154 MET cc_start: 0.8389 (mtt) cc_final: 0.8017 (mtt)
REVERT: A  158 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8367 (mmmm)
REVERT: A  172 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (tt)
REVERT: A  200 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (tt)
REVERT: A  203 ASP cc_start: 0.8292 (m-30) cc_final: 0.8089 (m-30)
REVERT: A  214 MET cc_start: 0.8472 (tpp) cc_final: 0.8245 (mmm)
REVERT: A  226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7311 (tm-30)
REVERT: A  256 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (mmm-85)
REVERT: A  270 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8152 (ttpp)
REVERT: A  272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7202 (mp)
REVERT: B   14 MET cc_start: 0.8383 (mtt) cc_final: 0.7992 (mtp)
REVERT: B   77 MET cc_start: 0.8611 (tpt) cc_final: 0.7987 (tpp)
REVERT: C   14 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6973 (ttp)
REVERT: C   18 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8289 (tt0)
REVERT: C   20 TYR cc_start: 0.8729 (t80) cc_final: 0.8527 (t80)
REVERT: C   48 CYS cc_start: 0.8823 (t) cc_final: 0.8613 (t)
REVERT: C   57 ILE cc_start: 0.8462 (mm) cc_final: 0.8200 (mp)
REVERT: D   18 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7520 (tp30)
REVERT: D   19 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7943 (mmt-90)
REVERT: D   38 HIS cc_start: 0.8698 (m-70) cc_final: 0.7821 (m-70)
REVERT: D   52 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8125 (tp40)
REVERT: D   62 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.6069 (p)
REVERT: D   67 LYS cc_start: 0.8107 (mptt) cc_final: 0.7895 (mmmt)
REVERT: D   72 ASP cc_start: 0.8153 (t0) cc_final: 0.7930 (t0)
REVERT: D   75 LEU cc_start: 0.8342 (mt) cc_final: 0.7994 (mt)
REVERT: D   95 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (p)
REVERT: D  103 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (mm-40)
REVERT: D  108 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6705 (mt-10)
REVERT: E   18 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (tp30)
REVERT: E   43 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (mt-10)
REVERT: E   52 GLN cc_start: 0.8192 (tm-30) cc_final: 0.6689 (tm-30)
REVERT: E   69 TYR cc_start: 0.8132 (m-10) cc_final: 0.7925 (m-80)
REVERT: E  111 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8102 (ttp-110)
REVERT: F   14 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6752 (tmm)
REVERT: F   19 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7857 (mmm160)
REVERT: F   20 TYR cc_start: 0.8393 (t80) cc_final: 0.7979 (t80)
REVERT: F   25 SER cc_start: 0.9279 (t) cc_final: 0.8998 (p)
REVERT: F   54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7749 (tm-30)
REVERT: F   55 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7198 (mp)
REVERT: F   92 HIS cc_start: 0.6308 (m-70) cc_final: 0.5962 (m90)
  outliers start: 149
  outliers final: 33
  residues processed: 356
  average time/residue: 0.3412
  time to fit residues: 153.9146
Evaluate side-chains
  271 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 214
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue    6 ARG
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   66 PHE
Chi-restraints excluded: chain A residue   74 ARG
Chi-restraints excluded: chain A residue   76 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   82 LYS
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   36 ARG
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   77 MET
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain D residue  108 GLU
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   18 GLU
Chi-restraints excluded: chain E residue   36 ARG
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   14 MET
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   66 SER
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   95 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A  87 GLN
A 290 HIS
A 306 HIS
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 ASN
C  92 HIS
C 121 ASN
D  13 GLN
E  32 GLN
** E  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  13 GLN
F  97 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.177035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135787 restraints weight = 15321.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.58
r_work: 0.3547 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096  10881  Z= 0.353
  Angle     :  0.820   9.577  15424  Z= 0.420
  Chirality :  0.043   0.233   1832
  Planarity :  0.008   0.123   1399
  Dihedral  : 24.948 173.757   3470
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 28.52
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.74 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  8.86 %
    Allowed  : 18.93 %
    Favored  : 72.21 %
  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: -2.06 (0.27), residues: 879
  helix: -0.61 (0.19), residues: 658
  sheet: -3.02 (1.07), residues: 26
  loop : -3.37 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 116 
 HIS   0.010   0.002   HIS C  92 
 PHE   0.040   0.003   PHE A 231 
 TYR   0.020   0.002   TYR C  28 
 ARG   0.007   0.001   ARG B  19 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 238
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7180 (mmtp)
REVERT: A    7 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6750 (m-40)
REVERT: A  115 THR cc_start: 0.9010 (m) cc_final: 0.8622 (p)
REVERT: A  165 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7936 (mtt180)
REVERT: A  272 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7136 (pp)
REVERT: B   22 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7796 (mtm110)
REVERT: B   69 TYR cc_start: 0.7953 (m-80) cc_final: 0.7722 (m-80)
REVERT: D   54 GLU cc_start: 0.7622 (tp30) cc_final: 0.7398 (tp30)
REVERT: E   42 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8364 (ttp-170)
REVERT: F   15 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6603 (pp)
REVERT: F   20 TYR cc_start: 0.8417 (t80) cc_final: 0.8135 (t80)
REVERT: F   47 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8001 (mttm)
  outliers start: 66
  outliers final: 23
  residues processed: 276
  average time/residue: 0.3068
  time to fit residues: 109.5952
Evaluate side-chains
  227 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   66 PHE
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue  104 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 77 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 121 ASN
** E  98 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 = 0.4249 r_free = 0.4249 target = 0.174728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132616 restraints weight = 15812.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 1.68
r_work: 0.3508 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  10881  Z= 0.346
  Angle     :  0.755  14.537  15424  Z= 0.382
  Chirality :  0.042   0.281   1832
  Planarity :  0.008   0.161   1399
  Dihedral  : 24.375 174.102   3369
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 26.27
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  8.53 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 20.94 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.38 (0.27), residues: 879
  helix: -0.16 (0.19), residues: 664
  sheet: -1.35 (1.34), residues: 14
  loop : -3.20 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 309 
 HIS   0.006   0.001   HIS A 121 
 PHE   0.032   0.003   PHE A 231 
 TYR   0.026   0.002   TYR C  28 
 ARG   0.009   0.001   ARG F 111 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 230
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7603 (mmtp)
REVERT: A  115 THR cc_start: 0.8980 (m) cc_final: 0.8750 (p)
REVERT: A  165 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7771 (mtt180)
REVERT: A  272 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7232 (pp)
REVERT: B   69 TYR cc_start: 0.7988 (m-80) cc_final: 0.7702 (m-80)
REVERT: C   42 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7881 (ttp-170)
REVERT: C   98 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8009 (mt0)
REVERT: D   19 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.7616 (mmm160)
REVERT: E   16 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7879 (pt)
REVERT: E   52 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6810 (tm-30)
REVERT: F   20 TYR cc_start: 0.8412 (t80) cc_final: 0.7963 (t80)
REVERT: F   47 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8096 (mttm)
  outliers start: 41
  outliers final: 25
  residues processed: 252
  average time/residue: 0.2984
  time to fit residues: 98.2629
Evaluate side-chains
  243 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LYS
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue   66 PHE
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   98 GLN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   95 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
B  32 GLN
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
** E  98 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 = 0.4250 r_free = 0.4250 target = 0.174752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.132889 restraints weight = 15562.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.67
r_work: 0.3510 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083  10881  Z= 0.337
  Angle     :  0.723   8.902  15424  Z= 0.367
  Chirality :  0.040   0.200   1832
  Planarity :  0.007   0.137   1399
  Dihedral  : 24.035 175.789   3362
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  7.51 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 22.28 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -1.09 (0.27), residues: 879
  helix: -0.04 (0.19), residues: 662
  sheet: -2.16 (1.08), residues: 26
  loop : -2.63 (0.45), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 116 
 HIS   0.007   0.001   HIS A 121 
 PHE   0.030   0.003   PHE A 231 
 TYR   0.024   0.002   TYR C  28 
 ARG   0.010   0.001   ARG F 111 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 236
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7310 (m-40) cc_final: 0.6876 (m-40)
REVERT: A  165 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7778 (mtt180)
REVERT: A  187 GLN cc_start: 0.8649 (mm110) cc_final: 0.8421 (mm-40)
REVERT: A  224 PRO cc_start: 0.6905 (Cg_exo) cc_final: 0.6655 (Cg_endo)
REVERT: B   47 LYS cc_start: 0.8460 (mttm) cc_final: 0.8259 (mttp)
REVERT: B   69 TYR cc_start: 0.7892 (m-10) cc_final: 0.7585 (m-80)
REVERT: B  119 ARG cc_start: 0.7890 (ptm-80) cc_final: 0.7587 (ptm-80)
REVERT: C   77 MET cc_start: 0.8521 (tpt) cc_final: 0.7939 (tpt)
REVERT: D   19 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7517 (mmm160)
REVERT: E   16 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (pt)
REVERT: E   52 GLN cc_start: 0.7455 (tm-30) cc_final: 0.6867 (tm-30)
REVERT: E   53 VAL cc_start: 0.8556 (t) cc_final: 0.8144 (t)
REVERT: E   92 HIS cc_start: 0.8092 (m170) cc_final: 0.7199 (m170)
REVERT: F   20 TYR cc_start: 0.8472 (t80) cc_final: 0.8145 (t80)
REVERT: F   47 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8178 (mttm)
  outliers start: 35
  outliers final: 22
  residues processed: 255
  average time/residue: 0.2902
  time to fit residues: 97.0309
Evaluate side-chains
  239 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 216
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue   66 PHE
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   95 THR
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   88 ILE
Chi-restraints excluded: chain F residue   95 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 94 optimal weight:   20.0000
   chunk 89 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 61 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 98 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
E  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.177532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.137232 restraints weight = 15584.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 1.62
r_work: 0.3561 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  10881  Z= 0.285
  Angle     :  0.692  10.198  15424  Z= 0.350
  Chirality :  0.039   0.195   1832
  Planarity :  0.007   0.125   1399
  Dihedral  : 23.666 173.215   3352
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 24.54
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.85 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.62 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.87 (0.28), residues: 879
  helix:  0.13 (0.19), residues: 664
  sheet: -1.60 (1.17), residues: 26
  loop : -2.70 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 116 
 HIS   0.006   0.001   HIS A 121 
 PHE   0.028   0.002   PHE A 231 
 TYR   0.021   0.002   TYR C  28 
 ARG   0.011   0.001   ARG C 119 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 229
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7296 (m-40) cc_final: 0.6740 (m-40)
REVERT: A  165 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7757 (mtt180)
REVERT: A  199 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6084 (mtt-85)
REVERT: A  212 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8083 (ttp80)
REVERT: A  224 PRO cc_start: 0.6788 (Cg_exo) cc_final: 0.6540 (Cg_endo)
REVERT: B   11 TYR cc_start: 0.7298 (t80) cc_final: 0.6890 (t80)
REVERT: C   12 ASP cc_start: 0.4364 (m-30) cc_final: 0.4112 (m-30)
REVERT: C   77 MET cc_start: 0.8513 (tpt) cc_final: 0.7926 (tpt)
REVERT: D   19 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7414 (mmm160)
REVERT: D   37 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7324 (mmmt)
REVERT: D   79 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7561 (mtt180)
REVERT: E   16 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7685 (pt)
REVERT: E   52 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6813 (tm-30)
REVERT: E   53 VAL cc_start: 0.8499 (t) cc_final: 0.8102 (t)
REVERT: E   92 HIS cc_start: 0.7970 (m170) cc_final: 0.7098 (m170)
REVERT: F   47 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8093 (mttm)
  outliers start: 35
  outliers final: 20
  residues processed: 251
  average time/residue: 0.2980
  time to fit residues: 97.9126
Evaluate side-chains
  242 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 220
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   67 LYS
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   65 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 29 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 93 optimal weight:   20.0000
   chunk 35 optimal weight:    0.0040
   chunk 20 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
A  57 ASN
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 121 ASN
** E  32 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 = 0.4266 r_free = 0.4266 target = 0.177446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.136839 restraints weight = 15650.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 1.61
r_work: 0.3546 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.5685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  10881  Z= 0.311
  Angle     :  0.707  10.284  15424  Z= 0.357
  Chirality :  0.040   0.194   1832
  Planarity :  0.007   0.124   1399
  Dihedral  : 23.555 175.048   3344
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 25.12
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  7.74 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 24.83 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.78 (0.28), residues: 879
  helix:  0.14 (0.19), residues: 664
  sheet: -1.46 (1.21), residues: 26
  loop : -2.46 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 116 
 HIS   0.008   0.001   HIS A 121 
 PHE   0.027   0.002   PHE A 231 
 TYR   0.024   0.003   TYR C  28 
 ARG   0.007   0.001   ARG E  36 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 217
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7127 (m-40) cc_final: 0.6617 (m-40)
REVERT: A  165 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7771 (mtt180)
REVERT: A  224 PRO cc_start: 0.6786 (Cg_exo) cc_final: 0.6515 (Cg_endo)
REVERT: D   19 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7366 (mmm160)
REVERT: D   37 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7308 (mmmt)
REVERT: D   79 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7778 (mtm-85)
REVERT: E   16 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7729 (pt)
REVERT: E   52 GLN cc_start: 0.7371 (tm-30) cc_final: 0.6885 (tm-30)
REVERT: E   53 VAL cc_start: 0.8526 (t) cc_final: 0.8093 (t)
REVERT: E   77 MET cc_start: 0.8411 (tpt) cc_final: 0.7727 (tpt)
REVERT: E   92 HIS cc_start: 0.7894 (m170) cc_final: 0.7111 (m170)
REVERT: F   47 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8202 (mttm)
  outliers start: 37
  outliers final: 21
  residues processed: 234
  average time/residue: 0.2951
  time to fit residues: 90.8708
Evaluate side-chains
  231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue  121 ASN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   65 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 103 GLN
D 121 ASN
** E  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 HIS ** 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 = 0.4274 r_free = 0.4274 target = 0.178158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.137605 restraints weight = 15678.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.62
r_work: 0.3556 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.5897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  10881  Z= 0.304
  Angle     :  0.700   8.868  15424  Z= 0.356
  Chirality :  0.039   0.243   1832
  Planarity :  0.007   0.116   1399
  Dihedral  : 23.500 178.055   3342
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 23.92
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.51 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 24.43 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.86 (0.28), residues: 879
  helix:  0.09 (0.19), residues: 658
  sheet:  0.66 (1.52), residues: 14
  loop : -2.61 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 266 
 HIS   0.009   0.001   HIS B  97 
 PHE   0.026   0.002   PHE A 231 
 TYR   0.023   0.003   TYR C  28 
 ARG   0.007   0.001   ARG A 199 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 219
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7187 (m-40) cc_final: 0.6672 (m-40)
REVERT: A  224 PRO cc_start: 0.6622 (Cg_exo) cc_final: 0.6380 (Cg_endo)
REVERT: B   11 TYR cc_start: 0.7139 (t80) cc_final: 0.6888 (t80)
REVERT: D   19 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7385 (mmm160)
REVERT: D   37 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7317 (mmmt)
REVERT: D   47 LYS cc_start: 0.8361 (mttm) cc_final: 0.8071 (mmtt)
REVERT: D   79 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7846 (mtm-85)
REVERT: E   16 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7710 (pt)
REVERT: E   52 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6858 (tm-30)
REVERT: E   77 MET cc_start: 0.8447 (tpt) cc_final: 0.7727 (tpt)
REVERT: E   92 HIS cc_start: 0.7896 (m170) cc_final: 0.7125 (m170)
REVERT: F   47 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8200 (mttm)
  outliers start: 32
  outliers final: 24
  residues processed: 233
  average time/residue: 0.2907
  time to fit residues: 89.3682
Evaluate side-chains
  238 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue  121 ASN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 92 optimal weight:    8.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4255 r_free = 0.4255 target = 0.176459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.135432 restraints weight = 15644.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.60
r_work: 0.3540 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.6000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  10881  Z= 0.341
  Angle     :  0.716   8.348  15424  Z= 0.363
  Chirality :  0.040   0.254   1832
  Planarity :  0.007   0.115   1399
  Dihedral  : 23.457 179.271   3342
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 25.49
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.28 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 26.71 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.85 (0.28), residues: 879
  helix:  0.07 (0.19), residues: 659
  sheet:  0.45 (1.43), residues: 14
  loop : -2.49 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 266 
 HIS   0.009   0.002   HIS B  97 
 PHE   0.026   0.002   PHE A 231 
 TYR   0.025   0.003   TYR C  28 
 ARG   0.008   0.001   ARG F  19 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7214 (m-40) cc_final: 0.6726 (m-40)
REVERT: A  224 PRO cc_start: 0.6721 (Cg_exo) cc_final: 0.6464 (Cg_endo)
REVERT: D   19 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7382 (mmm160)
REVERT: D   37 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7312 (mmmt)
REVERT: D   47 LYS cc_start: 0.8388 (mttm) cc_final: 0.8055 (mmtt)
REVERT: D   79 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7995 (mtm-85)
REVERT: E   16 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7775 (pt)
REVERT: E   52 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6846 (tm-30)
REVERT: E   92 HIS cc_start: 0.7917 (m170) cc_final: 0.7133 (m170)
REVERT: F   47 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8219 (mttm)
  outliers start: 28
  outliers final: 22
  residues processed: 225
  average time/residue: 0.2909
  time to fit residues: 86.4638
Evaluate side-chains
  225 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue  121 ASN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 29 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 121 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.177936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.137393 restraints weight = 15684.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.60
r_work: 0.3568 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.6271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  10881  Z= 0.322
  Angle     :  0.711   8.736  15424  Z= 0.362
  Chirality :  0.040   0.282   1832
  Planarity :  0.007   0.113   1399
  Dihedral  : 23.371 178.281   3342
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 24.02
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  7.05 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 26.17 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.81 (0.28), residues: 879
  helix:  0.09 (0.19), residues: 658
  sheet:  1.05 (1.54), residues: 14
  loop : -2.49 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 116 
 HIS   0.008   0.001   HIS A 121 
 PHE   0.025   0.002   PHE B  80 
 TYR   0.027   0.003   TYR C  28 
 ARG   0.008   0.001   ARG F  19 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ASN cc_start: 0.7321 (m-40) cc_final: 0.6958 (m-40)
REVERT: C   98 GLN cc_start: 0.8200 (tt0) cc_final: 0.7848 (tt0)
REVERT: D   37 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7457 (mmmt)
REVERT: D   47 LYS cc_start: 0.8336 (mttm) cc_final: 0.8057 (mmtt)
REVERT: D   79 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7710 (mtt180)
REVERT: E   16 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7695 (pt)
REVERT: E   52 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6830 (tm-30)
REVERT: E   92 HIS cc_start: 0.7906 (m170) cc_final: 0.7153 (m170)
REVERT: F   47 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8218 (mttm)
  outliers start: 24
  outliers final: 21
  residues processed: 228
  average time/residue: 0.2876
  time to fit residues: 87.2610
Evaluate side-chains
  228 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 206
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  100 GLU
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain D residue  121 ASN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0470
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.179567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.139326 restraints weight = 15627.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 1.61
r_work: 0.3591 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.6529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  10881  Z= 0.286
  Angle     :  0.727  21.452  15424  Z= 0.362
  Chirality :  0.040   0.300   1832
  Planarity :  0.008   0.185   1399
  Dihedral  : 23.285 177.578   3339
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 23.45
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  6.83 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 27.92 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.82 (0.28), residues: 879
  helix:  0.11 (0.19), residues: 658
  sheet:  1.45 (1.58), residues: 14
  loop : -2.61 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 116 
 HIS   0.009   0.001   HIS B  97 
 PHE   0.023   0.002   PHE B  80 
 TYR   0.022   0.003   TYR C  28 
 ARG   0.009   0.001   ARG F  19 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.8521 (tpt) cc_final: 0.7658 (tpt)
REVERT: C   90 LYS cc_start: 0.4749 (tmtt) cc_final: 0.4487 (tptp)
REVERT: D   37 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7242 (mmmt)
REVERT: D   47 LYS cc_start: 0.8251 (mttm) cc_final: 0.7966 (mmtt)
REVERT: D   79 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7800 (mtt180)
REVERT: E   16 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7651 (pt)
REVERT: E   52 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6811 (tm-30)
REVERT: E   92 HIS cc_start: 0.7813 (m170) cc_final: 0.7093 (m170)
REVERT: F   47 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8213 (mttm)
  outliers start: 22
  outliers final: 16
  residues processed: 221
  average time/residue: 0.2978
  time to fit residues: 87.8893
Evaluate side-chains
  212 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ARG
Chi-restraints excluded: chain A residue  109 CYS
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  202 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain D residue  121 ASN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 121 ASN
** E  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4269 r_free = 0.4269 target = 0.177645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136593 restraints weight = 15552.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.59
r_work: 0.3545 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.6552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  10881  Z= 0.355
  Angle     :  0.754  17.819  15424  Z= 0.375
  Chirality :  0.040   0.294   1832
  Planarity :  0.008   0.171   1399
  Dihedral  : 23.238 176.175   3339
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 24.70
  Ramachandran Plot:
    Outliers :  0.80 %
    Allowed  :  7.39 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 28.19 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.84 (0.28), residues: 879
  helix:  0.08 (0.19), residues: 662
  sheet:  1.26 (1.51), residues: 14
  loop : -2.60 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 116 
 HIS   0.009   0.001   HIS B  97 
 PHE   0.026   0.002   PHE B  80 
 TYR   0.028   0.003   TYR C  28 
 ARG   0.010   0.001   ARG E  36 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4937.23 seconds
wall clock time: 88 minutes 53.90 seconds (5333.90 seconds total)