Starting phenix.real_space_refine
on Thu May 15 21:51:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g88_29843/05_2025/8g88_29843.cif"
  }
  resolution = 4.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     336      5.49       5
     S      17      5.16       5
     C    7773      2.51       5
     N    2598      2.21       5
     O    3271      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13995
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 3417
          Classifications: {'DNA': 168}
          Link IDs: {'rna3p': 167}
    Chain: "J"
      Number of atoms: 3471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 3471
          Classifications: {'DNA': 168}
          Link IDs: {'rna3p': 167}
    Chain: "X"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1080
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 3, 'TRANS': 128}
          Chain breaks: 1
  Time building chain proxies: 7.76, per 1000 atoms: 0.55
  Number of scatterers: 13995
  At special positions: 0
  Unit cell: (82.11, 119.14, 175.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      17     16.00
     P     336     15.00
     O    3271      8.00
     N    2598      7.00
     C    7773      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: 3.12
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1674

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 10 sheets defined
      75.2% alpha, 2.5% beta
      155 base pairs and 306 stacking pairs defined.
    Time for finding SS restraints: 6.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.145A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.236A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 122
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.829A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.386A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'X' and resid 141 through 161
    Processing helix  chain 'X' and resid 163 through 176
    Processing helix  chain 'X' and resid 180 through 189
      removed outlier: 3.552A  pdb=" N   ILE X 184 " --> pdb=" O   SER X 180 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 193 through 211
      Proline residue:  X 202  - end of helix
    Processing helix  chain 'X' and resid 215 through 220
    Processing helix  chain 'X' and resid 239 through 249
    Processing helix  chain 'X' and resid 256 through 268
      removed outlier: 3.681A  pdb=" N   HIS X 262 " --> pdb=" O   GLN X 258 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 270 through 288
      removed outlier: 4.058A  pdb=" N   SER X 288 " --> pdb=" O   LYS X 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.003A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.691A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.144A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.770A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.763A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.057A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    492 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      370 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      155 basepair parallelities
      306 stacking parallelities
  Total time for adding SS restraints: 6.03

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2767
        1.33 -     1.45: 4835
        1.45 -     1.57: 6627
        1.57 -     1.69: 670
        1.69 -     1.81: 28
  Bond restraints: 14927
  Sorted by residual:
  bond pdb=" C1'  DC J -95 "
       pdb=" N1   DC J -95 "
    ideal  model  delta    sigma   weight residual
    1.490  1.549 -0.059 3.00e-02 1.11e+03 3.88e+00
  bond pdb=" O3'  DC I  80 "
       pdb=" P    DA I  81 "
    ideal  model  delta    sigma   weight residual
    1.607  1.636 -0.029 1.50e-02 4.44e+03 3.82e+00
  bond pdb=" C1'  DT J -75 "
       pdb=" N1   DT J -75 "
    ideal  model  delta    sigma   weight residual
    1.490  1.543 -0.053 3.00e-02 1.11e+03 3.10e+00
  bond pdb=" C1'  DT J -77 "
       pdb=" N1   DT J -77 "
    ideal  model  delta    sigma   weight residual
    1.490  1.542 -0.052 3.00e-02 1.11e+03 3.03e+00
  bond pdb=" O3'  DC I  82 "
       pdb=" P    DA I  83 "
    ideal  model  delta    sigma   weight residual
    1.607  1.632 -0.025 1.50e-02 4.44e+03 2.85e+00
  ... (remaining 14922 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 21419
        2.36 -     4.72: 147
        4.72 -     7.07: 26
        7.07 -     9.43: 3
        9.43 -    11.79: 1
  Bond angle restraints: 21596
  Sorted by residual:
  angle pdb=" C4'  DC I  82 "
        pdb=" C3'  DC I  82 "
        pdb=" O3'  DC I  82 "
      ideal   model   delta    sigma   weight residual
     110.00  117.36   -7.36 1.50e+00 4.44e-01 2.41e+01
  angle pdb=" O3'  DC I  82 "
        pdb=" C3'  DC I  82 "
        pdb=" C2'  DC I  82 "
      ideal   model   delta    sigma   weight residual
     111.50  104.38    7.12 1.50e+00 4.44e-01 2.25e+01
  angle pdb=" O3'  DT J -77 "
        pdb=" P    DG J -76 "
        pdb=" O5'  DG J -76 "
      ideal   model   delta    sigma   weight residual
     104.00   97.05    6.95 1.50e+00 4.44e-01 2.15e+01
  angle pdb=" O3'  DT J -75 "
        pdb=" P    DG J -74 "
        pdb=" O5'  DG J -74 "
      ideal   model   delta    sigma   weight residual
     104.00   97.08    6.92 1.50e+00 4.44e-01 2.13e+01
  angle pdb=" O3'  DG J -76 "
        pdb=" P    DT J -75 "
        pdb=" O5'  DT J -75 "
      ideal   model   delta    sigma   weight residual
     104.00   97.10    6.90 1.50e+00 4.44e-01 2.12e+01
  ... (remaining 21591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 6595
       35.89 -    71.78: 1596
       71.78 -   107.66: 18
      107.66 -   143.55: 0
      143.55 -   179.44: 3
  Dihedral angle restraints: 8212
    sinusoidal: 5626
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" C4'  DT I  20 "
           pdb=" C3'  DT I  20 "
           pdb=" O3'  DT I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.44 -179.44     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I  81 "
           pdb=" C3'  DA I  81 "
           pdb=" O3'  DA I  81 "
           pdb=" P    DC I  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.15 -176.15     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC I  80 "
           pdb=" C3'  DC I  80 "
           pdb=" O3'  DC I  80 "
           pdb=" P    DA I  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   16.00 -156.00     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 8209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 2062
       0.041 -    0.082: 331
       0.082 -    0.123: 51
       0.123 -    0.165: 9
       0.165 -    0.206: 4
  Chirality restraints: 2457
  Sorted by residual:
  chirality pdb=" C3'  DC I  72 "
            pdb=" C4'  DC I  72 "
            pdb=" O3'  DC I  72 "
            pdb=" C2'  DC I  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C3'  DT J -73 "
            pdb=" C4'  DT J -73 "
            pdb=" O3'  DT J -73 "
            pdb=" C2'  DT J -73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" C3'  DC I  74 "
            pdb=" C4'  DC I  74 "
            pdb=" O3'  DC I  74 "
            pdb=" C2'  DC I  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 9.14e-01
  ... (remaining 2454 not shown)

  Planarity restraints: 1569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.55e+00
        pdb=" N   PRO G  80 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO C  80 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS X 254 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO X 255 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO X 255 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO X 255 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1566 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2950
        2.80 -     3.33: 12263
        3.33 -     3.85: 28072
        3.85 -     4.38: 34764
        4.38 -     4.90: 46610
  Nonbonded interactions: 124659
  Sorted by model distance:
  nonbonded pdb=" O   GLN X 155 "
            pdb=" OG1 THR X 159 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" NE  ARG X 157 "
            pdb=" OE2 GLU X 188 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OP2  DA I  88 "
            pdb=" ND2 ASN X 196 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" NH2 ARG X 157 "
            pdb=" OE1 GLU X 188 "
     model   vdw
     2.305 3.120
  ... (remaining 124654 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = (chain 'F' and resid 22 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.96
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     36.780
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14927  Z= 0.175
  Angle     :  0.598  11.791  21596  Z= 0.361
  Chirality :  0.033   0.206   2457
  Planarity :  0.004   0.047   1569
  Dihedral  : 27.716 179.439   6538
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.78 %
    Favored  : 82.29 %
  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:  1.45 (0.26), residues: 871
  helix:  1.36 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.12 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP X 277 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.011   0.001   PHE X 187 
 TYR   0.010   0.001   TYR B  51 
 ARG   0.004   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22233 (  862)
  hydrogen bonds       : angle       8.29165 ( 2188)
  covalent geometry    : bond        0.00380 (14927)
  covalent geometry    : angle       0.59770 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 1.096 
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: 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: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9112 (mt) cc_final: 0.8637 (mt)
REVERT: B   62 LEU cc_start: 0.8727 (mt) cc_final: 0.8335 (mt)
REVERT: C   97 LEU cc_start: 0.8888 (mt) cc_final: 0.7252 (mt)
REVERT: D   66 VAL cc_start: 0.8533 (t) cc_final: 0.7907 (p)
REVERT: E   97 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7047 (mt-10)
REVERT: E  100 LEU cc_start: 0.8604 (mt) cc_final: 0.7877 (mm)
REVERT: E  130 ILE cc_start: 0.7737 (mt) cc_final: 0.7519 (mm)
REVERT: F   58 LEU cc_start: 0.7487 (tp) cc_final: 0.7112 (tp)
REVERT: F   62 LEU cc_start: 0.8944 (mt) cc_final: 0.7987 (mt)
REVERT: F   97 LEU cc_start: 0.7684 (tp) cc_final: 0.7412 (tp)
REVERT: H   70 ILE cc_start: 0.8916 (mt) cc_final: 0.8643 (mm)
REVERT: H   97 LEU cc_start: 0.7747 (mt) cc_final: 0.7464 (mt)
  outliers start: 7
  outliers final: 0
  residues processed: 148
  average time/residue: 0.3678
  time to fit residues: 71.6686
Evaluate side-chains
  62 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 91 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
** F  25 ASN ** 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 = 0.2905 r_free = 0.2905 target = 0.030543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.024589 restraints weight = 251829.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.025029 restraints weight = 172346.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.025324 restraints weight = 130743.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084  14927  Z= 0.301
  Angle     :  0.721   9.076  21596  Z= 0.419
  Chirality :  0.040   0.208   2457
  Planarity :  0.005   0.046   1569
  Dihedral  : 31.511 175.995   4747
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  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:  2.18 (0.27), residues: 871
  helix:  1.94 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.04 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP X 277 
 HIS   0.007   0.002   HIS E 113 
 PHE   0.030   0.002   PHE X 278 
 TYR   0.016   0.002   TYR B  88 
 ARG   0.007   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08563 (  862)
  hydrogen bonds       : angle       3.56720 ( 2188)
  covalent geometry    : bond        0.00672 (14927)
  covalent geometry    : angle       0.72061 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.938 
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: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9401 (tpt) cc_final: 0.9089 (tpp)
REVERT: D   59 MET cc_start: 0.9640 (mmp) cc_final: 0.9247 (mmm)
REVERT: E   97 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8751 (mt-10)
REVERT: H   59 MET cc_start: 0.9676 (mmp) cc_final: 0.9274 (mmm)
REVERT: H   70 ILE cc_start: 0.9704 (mt) cc_final: 0.9462 (tp)
REVERT: H   97 LEU cc_start: 0.8295 (mt) cc_final: 0.8075 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.3556
  time to fit residues: 38.5221
Evaluate side-chains
  41 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 115 optimal weight:    8.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
** F  25 ASN ** 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 = 0.2905 r_free = 0.2905 target = 0.030558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.024460 restraints weight = 248714.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.024890 restraints weight = 167907.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.025211 restraints weight = 126681.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  14927  Z= 0.185
  Angle     :  0.599   7.952  21596  Z= 0.356
  Chirality :  0.034   0.169   2457
  Planarity :  0.004   0.046   1569
  Dihedral  : 31.281 175.822   4747
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.38 (0.27), residues: 871
  helix:  2.04 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.18 (0.40), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X 277 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.023   0.002   PHE A 104 
 TYR   0.011   0.001   TYR D  37 
 ARG   0.006   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  862)
  hydrogen bonds       : angle       3.28396 ( 2188)
  covalent geometry    : bond        0.00403 (14927)
  covalent geometry    : angle       0.59941 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.970 
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: A  104 PHE cc_start: 0.9683 (m-80) cc_final: 0.9411 (m-80)
REVERT: B   84 MET cc_start: 0.9323 (tpt) cc_final: 0.8988 (tpp)
REVERT: E   50 GLU cc_start: 0.9552 (mp0) cc_final: 0.9271 (mp0)
REVERT: E   86 SER cc_start: 0.9382 (p) cc_final: 0.9146 (p)
REVERT: E   90 MET cc_start: 0.9485 (mmp) cc_final: 0.9239 (ptp)
REVERT: E  104 PHE cc_start: 0.9545 (m-10) cc_final: 0.9298 (m-10)
REVERT: F   84 MET cc_start: 0.9580 (tpp) cc_final: 0.9359 (tpt)
REVERT: H   59 MET cc_start: 0.9680 (mmp) cc_final: 0.9271 (mmm)
REVERT: H   70 ILE cc_start: 0.9684 (mt) cc_final: 0.9470 (tp)
REVERT: H   97 LEU cc_start: 0.8078 (mt) cc_final: 0.7830 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.3379
  time to fit residues: 29.8026
Evaluate side-chains
  39 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 87 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  44 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 = 0.2819 r_free = 0.2819 target = 0.026330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.020693 restraints weight = 286327.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.021167 restraints weight = 178238.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.021496 restraints weight = 125925.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.7151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100  14927  Z= 0.384
  Angle     :  0.787   9.350  21596  Z= 0.458
  Chirality :  0.043   0.176   2457
  Planarity :  0.007   0.078   1569
  Dihedral  : 32.919 175.260   4747
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 29.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.43 (0.27), residues: 871
  helix:  1.33 (0.19), residues: 647
  sheet:  None (None), residues: 0
  loop :  0.05 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP X 277 
 HIS   0.006   0.002   HIS B  75 
 PHE   0.017   0.003   PHE B  61 
 TYR   0.024   0.003   TYR C  50 
 ARG   0.008   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12991 (  862)
  hydrogen bonds       : angle       4.23544 ( 2188)
  covalent geometry    : bond        0.00843 (14927)
  covalent geometry    : angle       0.78665 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9321 (m-80) cc_final: 0.9092 (m-10)
REVERT: B   62 LEU cc_start: 0.9568 (mm) cc_final: 0.9352 (mp)
REVERT: B   84 MET cc_start: 0.9108 (tpt) cc_final: 0.8427 (tpp)
REVERT: E  104 PHE cc_start: 0.9329 (m-10) cc_final: 0.8773 (m-10)
REVERT: H   59 MET cc_start: 0.9618 (mmp) cc_final: 0.8805 (mmm)
REVERT: H   97 LEU cc_start: 0.8837 (mt) cc_final: 0.8610 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.3364
  time to fit residues: 21.8330
Evaluate side-chains
  30 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 112 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 100 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 116 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.027733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.021951 restraints weight = 266186.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.022436 restraints weight = 164683.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.022760 restraints weight = 116262.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.7139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14927  Z= 0.204
  Angle     :  0.649  15.053  21596  Z= 0.379
  Chirality :  0.036   0.175   2457
  Planarity :  0.005   0.079   1569
  Dihedral  : 32.217 171.906   4747
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.60 %
    Favored  : 98.27 %
  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:  1.82 (0.28), residues: 871
  helix:  1.65 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.01 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X 277 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.016   0.002   PHE B  61 
 TYR   0.014   0.002   TYR G  50 
 ARG   0.005   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06201 (  862)
  hydrogen bonds       : angle       3.68216 ( 2188)
  covalent geometry    : bond        0.00445 (14927)
  covalent geometry    : angle       0.64905 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9450 (m-80) cc_final: 0.9214 (m-10)
REVERT: B   84 MET cc_start: 0.9300 (tpt) cc_final: 0.8632 (tpp)
REVERT: D   62 PHE cc_start: 0.9791 (t80) cc_final: 0.9585 (t80)
REVERT: E   86 SER cc_start: 0.9425 (p) cc_final: 0.9066 (p)
REVERT: E  104 PHE cc_start: 0.9374 (m-10) cc_final: 0.8828 (m-10)
REVERT: H   59 MET cc_start: 0.9554 (mmp) cc_final: 0.8743 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.3007
  time to fit residues: 19.7471
Evaluate side-chains
  31 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 70 optimal weight:   30.0000
   chunk 111 optimal weight:   10.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.025814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.020247 restraints weight = 293183.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.020699 restraints weight = 184779.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.021009 restraints weight = 131897.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.8549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.084  14927  Z= 0.357
  Angle     :  0.761  14.747  21596  Z= 0.445
  Chirality :  0.042   0.169   2457
  Planarity :  0.006   0.052   1569
  Dihedral  : 33.109 175.486   4747
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 29.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.26 %
    Favored  : 97.60 %
  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:  1.00 (0.27), residues: 871
  helix:  1.07 (0.20), residues: 651
  sheet:  None (None), residues: 0
  loop : -0.35 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.003   TRP X 207 
 HIS   0.004   0.002   HIS B  75 
 PHE   0.021   0.003   PHE A  67 
 TYR   0.018   0.003   TYR D 118 
 ARG   0.010   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12554 (  862)
  hydrogen bonds       : angle       4.24642 ( 2188)
  covalent geometry    : bond        0.00780 (14927)
  covalent geometry    : angle       0.76124 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9645 (m-80) cc_final: 0.9411 (m-10)
REVERT: B   84 MET cc_start: 0.9094 (tpt) cc_final: 0.8765 (tpp)
REVERT: E   90 MET cc_start: 0.9589 (ptp) cc_final: 0.9313 (mmp)
REVERT: E  104 PHE cc_start: 0.9388 (m-10) cc_final: 0.8822 (m-80)
REVERT: F   37 LEU cc_start: 0.9624 (mm) cc_final: 0.9379 (pp)
REVERT: H   59 MET cc_start: 0.9729 (mmp) cc_final: 0.9339 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.2987
  time to fit residues: 18.2697
Evaluate side-chains
  31 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 96 optimal weight:    7.9990
   chunk 98 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 108 optimal weight:   40.0000
   chunk 106 optimal weight:   40.0000
   chunk 70 optimal weight:   30.0000
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
H  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.026534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.020889 restraints weight = 280443.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.021366 restraints weight = 171391.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.021688 restraints weight = 120044.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.8748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074  14927  Z= 0.256
  Angle     :  0.680   8.831  21596  Z= 0.400
  Chirality :  0.038   0.149   2457
  Planarity :  0.005   0.046   1569
  Dihedral  : 32.798 171.393   4747
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 20.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  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:  1.27 (0.28), residues: 871
  helix:  1.26 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.27 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 277 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.018   0.002   PHE C  25 
 TYR   0.011   0.002   TYR F  88 
 ARG   0.008   0.001   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08164 (  862)
  hydrogen bonds       : angle       3.98663 ( 2188)
  covalent geometry    : bond        0.00555 (14927)
  covalent geometry    : angle       0.68021 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9659 (m-80) cc_final: 0.9417 (m-10)
REVERT: B   84 MET cc_start: 0.9240 (tpt) cc_final: 0.8937 (tpp)
REVERT: E   90 MET cc_start: 0.9577 (ptp) cc_final: 0.9319 (mmp)
REVERT: E  104 PHE cc_start: 0.9427 (m-10) cc_final: 0.9043 (m-80)
REVERT: H   59 MET cc_start: 0.9704 (mmp) cc_final: 0.9327 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.3664
  time to fit residues: 21.3780
Evaluate side-chains
  31 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 114 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.026240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.020626 restraints weight = 274750.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.021110 restraints weight = 165795.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.021417 restraints weight = 114584.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.9357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083  14927  Z= 0.277
  Angle     :  0.690   8.565  21596  Z= 0.407
  Chirality :  0.038   0.153   2457
  Planarity :  0.005   0.049   1569
  Dihedral  : 32.913 174.117   4747
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 24.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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:  1.11 (0.28), residues: 871
  helix:  1.17 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 277 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.020   0.002   PHE A  67 
 TYR   0.010   0.002   TYR D 118 
 ARG   0.006   0.001   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09516 (  862)
  hydrogen bonds       : angle       4.02674 ( 2188)
  covalent geometry    : bond        0.00606 (14927)
  covalent geometry    : angle       0.69024 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9541 (m-80) cc_final: 0.9281 (m-80)
REVERT: B   84 MET cc_start: 0.9221 (tpt) cc_final: 0.8679 (tpp)
REVERT: E   86 SER cc_start: 0.9417 (p) cc_final: 0.9155 (p)
REVERT: E   90 MET cc_start: 0.9449 (ptp) cc_final: 0.9202 (ptt)
REVERT: E  104 PHE cc_start: 0.9447 (m-10) cc_final: 0.8850 (m-80)
REVERT: H   59 MET cc_start: 0.9675 (mmp) cc_final: 0.9004 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.3267
  time to fit residues: 18.8487
Evaluate side-chains
  30 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.025724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2537 r_free = 0.2537 target = 0.020245 restraints weight = 288909.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.020619 restraints weight = 188610.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.020870 restraints weight = 138841.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.9675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074  14927  Z= 0.267
  Angle     :  0.687   8.962  21596  Z= 0.403
  Chirality :  0.038   0.191   2457
  Planarity :  0.005   0.043   1569
  Dihedral  : 32.959 172.539   4747
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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:  1.05 (0.28), residues: 871
  helix:  1.12 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.38 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP X 277 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.017   0.002   PHE C  25 
 TYR   0.010   0.002   TYR F  98 
 ARG   0.006   0.001   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08802 (  862)
  hydrogen bonds       : angle       4.04069 ( 2188)
  covalent geometry    : bond        0.00581 (14927)
  covalent geometry    : angle       0.68652 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9649 (m-80) cc_final: 0.9407 (m-80)
REVERT: B   84 MET cc_start: 0.9033 (tpt) cc_final: 0.8734 (tpp)
REVERT: D   34 TYR cc_start: 0.9491 (m-80) cc_final: 0.9195 (m-80)
REVERT: E  104 PHE cc_start: 0.9433 (m-10) cc_final: 0.9021 (m-80)
REVERT: H   59 MET cc_start: 0.9739 (mmp) cc_final: 0.9371 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.3257
  time to fit residues: 20.2395
Evaluate side-chains
  37 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 88 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.025693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.020172 restraints weight = 287749.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.020630 restraints weight = 172532.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.020931 restraints weight = 119652.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.9974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074  14927  Z= 0.265
  Angle     :  0.686   8.804  21596  Z= 0.403
  Chirality :  0.038   0.158   2457
  Planarity :  0.005   0.047   1569
  Dihedral  : 33.042 174.132   4747
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 23.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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:  1.08 (0.28), residues: 871
  helix:  1.14 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.36 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP X 207 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.016   0.002   PHE C  25 
 TYR   0.010   0.002   TYR F  98 
 ARG   0.006   0.001   ARG H  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08990 (  862)
  hydrogen bonds       : angle       4.05777 ( 2188)
  covalent geometry    : bond        0.00577 (14927)
  covalent geometry    : angle       0.68604 (21596)

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9575 (m-80) cc_final: 0.9349 (m-80)
REVERT: B   84 MET cc_start: 0.8961 (tpt) cc_final: 0.8672 (tpp)
REVERT: C  110 ASN cc_start: 0.9034 (t0) cc_final: 0.8761 (t0)
REVERT: D   34 TYR cc_start: 0.9454 (m-80) cc_final: 0.9202 (m-80)
REVERT: E  104 PHE cc_start: 0.9418 (m-10) cc_final: 0.9032 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.3248
  time to fit residues: 21.2533
Evaluate side-chains
  35 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 87 optimal weight:   10.0000
   chunk 71 optimal weight:    0.4980
   chunk 63 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
D  44 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.027055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.021378 restraints weight = 270451.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.021869 restraints weight = 160663.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022187 restraints weight = 110493.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.9745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14927  Z= 0.175
  Angle     :  0.640  10.249  21596  Z= 0.375
  Chirality :  0.036   0.166   2457
  Planarity :  0.005   0.050   1569
  Dihedral  : 32.492 173.297   4747
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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:  1.51 (0.28), residues: 871
  helix:  1.44 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.16 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 277 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.015   0.002   PHE C  25 
 TYR   0.010   0.001   TYR F  88 
 ARG   0.006   0.000   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05287 (  862)
  hydrogen bonds       : angle       3.73753 ( 2188)
  covalent geometry    : bond        0.00377 (14927)
  covalent geometry    : angle       0.64013 (21596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3136.05 seconds
wall clock time: 56 minutes 12.43 seconds (3372.43 seconds total)