Starting phenix.real_space_refine
on Thu Jul 31 16:36:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g88_29843/07_2025/8g88_29843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g88_29843/07_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_29843/07_2025/8g88_29843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2025/8g88_29843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_2025/8g88_29843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g88_29843/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.01, per 1000 atoms: 0.64
  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: 3.27
  Conformation dependent library (CDL) restraints added in 1.1 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: 7.79
  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: 6.82

  Time building geometry restraints manager: 3.97 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:             0.350
  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:             0.020
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     41.560
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.070
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.230
-------------------------------------------------------------------------------
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  : 1.055 
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: 0.3802
  time to fit residues: 74.4811
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  : 1.177 
-------------------------------------------------------------------------------
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 = 0.030542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.024578 restraints weight = 251834.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.025023 restraints weight = 172656.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.025320 restraints weight = 130825.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
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       0.72060 (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  : 1.132 
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: 0.9400 (tpt) cc_final: 0.9090 (tpp)
REVERT: D   59 MET cc_start: 0.9639 (mmp) cc_final: 0.9247 (mmm)
REVERT: E   97 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8750 (mt-10)
REVERT: H   59 MET cc_start: 0.9676 (mmp) cc_final: 0.9274 (mmm)
REVERT: H   70 ILE cc_start: 0.9703 (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: 0.3726
  time to fit residues: 40.4115
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  : 1.215 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 115 optimal weight:    8.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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  93 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.029208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.023296 restraints weight = 255826.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.023705 restraints weight = 171059.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.023984 restraints weight = 128051.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  14927  Z= 0.224
  Angle     :  0.646   8.803  21596  Z= 0.380
  Chirality :  0.036   0.181   2457
  Planarity :  0.005   0.041   1569
  Dihedral  : 31.655 175.254   4747
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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:  2.14 (0.27), residues: 871
  helix:  1.82 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.26 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X 277 
 HIS   0.005   0.001   HIS X 262 
 PHE   0.031   0.002   PHE A 104 
 TYR   0.011   0.002   TYR F  98 
 ARG   0.007   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06404 (  862)
  hydrogen bonds       : angle       3.46849 ( 2188)
  covalent geometry    : bond        0.00488 (14927)
  covalent geometry    : angle       0.64636 (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
  63 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.048 
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   50 GLU cc_start: 0.9444 (pt0) cc_final: 0.9185 (pt0)
REVERT: A  104 PHE cc_start: 0.9683 (m-80) cc_final: 0.9418 (m-80)
REVERT: B   84 MET cc_start: 0.9231 (tpt) cc_final: 0.8860 (tpp)
REVERT: D   62 PHE cc_start: 0.9779 (t80) cc_final: 0.9505 (t80)
REVERT: E   86 SER cc_start: 0.9433 (p) cc_final: 0.9174 (p)
REVERT: E   90 MET cc_start: 0.9500 (mmp) cc_final: 0.9242 (ptp)
REVERT: E  120 MET cc_start: 0.9289 (mtm) cc_final: 0.9041 (mtt)
REVERT: H   54 LYS cc_start: 0.9503 (tptt) cc_final: 0.9274 (tptt)
REVERT: H   59 MET cc_start: 0.9708 (mmp) cc_final: 0.9312 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.3658
  time to fit residues: 31.5269
Evaluate side-chains
  38 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 113 optimal weight:    0.1980
   chunk 80 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    4.4388

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 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 = 0.2854 r_free = 0.2854 target = 0.027909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.022097 restraints weight = 263378.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022581 restraints weight = 166249.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.022911 restraints weight = 118263.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.6504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  14927  Z= 0.249
  Angle     :  0.650   8.986  21596  Z= 0.382
  Chirality :  0.037   0.220   2457
  Planarity :  0.005   0.047   1569
  Dihedral  : 32.024 173.600   4747
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    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:  2.12 (0.28), residues: 871
  helix:  1.79 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop :  0.36 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP X 277 
 HIS   0.008   0.002   HIS D 106 
 PHE   0.013   0.002   PHE A 104 
 TYR   0.020   0.002   TYR C  50 
 ARG   0.015   0.001   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07993 (  862)
  hydrogen bonds       : angle       3.63653 ( 2188)
  covalent geometry    : bond        0.00546 (14927)
  covalent geometry    : angle       0.65026 (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
  54 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9346 (m-80) cc_final: 0.9125 (m-80)
REVERT: B   84 MET cc_start: 0.9277 (tpt) cc_final: 0.8592 (tpp)
REVERT: D   59 MET cc_start: 0.9167 (tpt) cc_final: 0.8651 (tpp)
REVERT: D   62 PHE cc_start: 0.9710 (t80) cc_final: 0.9406 (t80)
REVERT: E  104 PHE cc_start: 0.9362 (m-10) cc_final: 0.8991 (m-80)
REVERT: H   59 MET cc_start: 0.9516 (mmp) cc_final: 0.8679 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.3250
  time to fit residues: 24.9807
Evaluate side-chains
  32 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0040
   chunk 15 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 116 optimal weight:    7.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    5.2000

-------------------------------------------------------------------------------
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**
D  44 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.026973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.021241 restraints weight = 280803.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.021726 restraints weight = 172139.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.022050 restraints weight = 120101.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.7691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  14927  Z= 0.275
  Angle     :  0.678  10.328  21596  Z= 0.397
  Chirality :  0.038   0.217   2457
  Planarity :  0.005   0.051   1569
  Dihedral  : 32.326 173.803   4747
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.13 %
    Favored  : 97.74 %
  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:  1.72 (0.28), residues: 871
  helix:  1.54 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop :  0.10 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP X 277 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.020   0.002   PHE A  67 
 TYR   0.014   0.002   TYR H  34 
 ARG   0.006   0.001   ARG B  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09020 (  862)
  hydrogen bonds       : angle       3.82870 ( 2188)
  covalent geometry    : bond        0.00599 (14927)
  covalent geometry    : angle       0.67817 (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
  40 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9429 (m-80) cc_final: 0.9185 (m-10)
REVERT: B   84 MET cc_start: 0.9251 (tpt) cc_final: 0.8617 (tpp)
REVERT: D   59 MET cc_start: 0.9183 (tpt) cc_final: 0.8645 (tpp)
REVERT: D   62 PHE cc_start: 0.9707 (t80) cc_final: 0.9378 (t80)
REVERT: E   86 SER cc_start: 0.9486 (p) cc_final: 0.8932 (p)
REVERT: E  104 PHE cc_start: 0.9384 (m-10) cc_final: 0.8956 (m-80)
REVERT: H   59 MET cc_start: 0.9527 (mmp) cc_final: 0.8763 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.3115
  time to fit residues: 18.4183
Evaluate side-chains
  30 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 70 optimal weight:    0.2980
   chunk 111 optimal weight:    6.9990
   overall best weight:    4.2588

-------------------------------------------------------------------------------
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**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 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 = 0.2847 r_free = 0.2847 target = 0.027350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.021546 restraints weight = 277030.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.022031 restraints weight = 170727.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.022365 restraints weight = 119494.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.8092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  14927  Z= 0.234
  Angle     :  0.638   9.262  21596  Z= 0.378
  Chirality :  0.036   0.149   2457
  Planarity :  0.005   0.047   1569
  Dihedral  : 32.209 172.852   4747
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.86 %
    Favored  : 98.00 %
  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:  1.81 (0.28), residues: 871
  helix:  1.63 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop :  0.04 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP X 277 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.030   0.002   PHE C  25 
 TYR   0.015   0.002   TYR F  88 
 ARG   0.005   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07507 (  862)
  hydrogen bonds       : angle       3.73760 ( 2188)
  covalent geometry    : bond        0.00511 (14927)
  covalent geometry    : angle       0.63770 (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
  40 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9654 (m-80) cc_final: 0.9396 (m-80)
REVERT: B   84 MET cc_start: 0.9196 (tpt) cc_final: 0.8766 (tpp)
REVERT: D   59 MET cc_start: 0.9600 (tpt) cc_final: 0.9225 (tpp)
REVERT: E  104 PHE cc_start: 0.9427 (m-10) cc_final: 0.9166 (m-80)
REVERT: H   59 MET cc_start: 0.9683 (mmp) cc_final: 0.9311 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 0.3573
  time to fit residues: 20.7003
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  : 1.124 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 108 optimal weight:   30.0000
   chunk 106 optimal weight:   30.0000
   chunk 70 optimal weight:   30.0000
   chunk 71 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   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**
** H 106 HIS ** 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 = 0.2813 r_free = 0.2813 target = 0.025571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2514 r_free = 0.2514 target = 0.019602 restraints weight = 301420.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.020063 restraints weight = 186120.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.020377 restraints weight = 131625.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.9316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.085  14927  Z= 0.371
  Angle     :  0.765   9.261  21596  Z= 0.448
  Chirality :  0.042   0.171   2457
  Planarity :  0.007   0.058   1569
  Dihedral  : 33.116 175.162   4747
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 31.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  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:  0.97 (0.27), residues: 871
  helix:  1.01 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.23 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP X 207 
 HIS   0.004   0.002   HIS E 113 
 PHE   0.039   0.003   PHE C  25 
 TYR   0.019   0.003   TYR D 118 
 ARG   0.007   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13066 (  862)
  hydrogen bonds       : angle       4.32903 ( 2188)
  covalent geometry    : bond        0.00813 (14927)
  covalent geometry    : angle       0.76499 (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
  36 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9515 (m-80) cc_final: 0.9233 (m-80)
REVERT: B   84 MET cc_start: 0.9026 (tpt) cc_final: 0.8397 (tpp)
REVERT: D   34 TYR cc_start: 0.9264 (m-80) cc_final: 0.8850 (m-80)
REVERT: D   59 MET cc_start: 0.9350 (tpt) cc_final: 0.8783 (tpp)
REVERT: D   62 PHE cc_start: 0.9786 (t80) cc_final: 0.9300 (t80)
REVERT: E   86 SER cc_start: 0.9491 (p) cc_final: 0.9088 (p)
REVERT: E   90 MET cc_start: 0.9269 (mmp) cc_final: 0.9036 (ptp)
REVERT: E  104 PHE cc_start: 0.9432 (m-10) cc_final: 0.8925 (m-80)
REVERT: H   59 MET cc_start: 0.9648 (mmp) cc_final: 0.8867 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.2866
  time to fit residues: 15.7898
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  : 1.021 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 113 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** E  68 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 = 0.2845 r_free = 0.2845 target = 0.027029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.021264 restraints weight = 269501.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.021754 restraints weight = 160240.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.022083 restraints weight = 110401.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.9249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  14927  Z= 0.224
  Angle     :  0.660   8.680  21596  Z= 0.389
  Chirality :  0.037   0.150   2457
  Planarity :  0.005   0.048   1569
  Dihedral  : 32.638 172.397   4747
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: 871
  helix:  1.32 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.15 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP X 277 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.019   0.002   PHE C  25 
 TYR   0.012   0.002   TYR H  37 
 ARG   0.005   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07189 (  862)
  hydrogen bonds       : angle       3.89258 ( 2188)
  covalent geometry    : bond        0.00487 (14927)
  covalent geometry    : angle       0.65999 (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
  42 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9500 (m-80) cc_final: 0.9235 (m-10)
REVERT: B   84 MET cc_start: 0.9099 (tpt) cc_final: 0.8561 (tpp)
REVERT: D   34 TYR cc_start: 0.9210 (m-80) cc_final: 0.8688 (m-80)
REVERT: D   59 MET cc_start: 0.9245 (tpt) cc_final: 0.8641 (tpp)
REVERT: D   62 PHE cc_start: 0.9793 (t80) cc_final: 0.9401 (t80)
REVERT: E   86 SER cc_start: 0.9499 (p) cc_final: 0.9084 (p)
REVERT: E   90 MET cc_start: 0.9262 (mmp) cc_final: 0.9041 (ptp)
REVERT: E  104 PHE cc_start: 0.9497 (m-10) cc_final: 0.9010 (m-80)
REVERT: G  110 ASN cc_start: 0.9234 (t0) cc_final: 0.8989 (p0)
REVERT: H   56 MET cc_start: 0.9251 (tpt) cc_final: 0.9043 (tpt)
REVERT: H   59 MET cc_start: 0.9592 (mmp) cc_final: 0.8796 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.3268
  time to fit residues: 20.1066
Evaluate side-chains
  34 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 101 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 113 optimal weight:    0.0570
   overall best weight:    4.0106

-------------------------------------------------------------------------------
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**
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.026181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.020581 restraints weight = 289129.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.020971 restraints weight = 188029.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.021233 restraints weight = 138076.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.9515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  14927  Z= 0.236
  Angle     :  0.660   8.535  21596  Z= 0.389
  Chirality :  0.037   0.209   2457
  Planarity :  0.005   0.046   1569
  Dihedral  : 32.564 174.171   4747
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.48 (0.28), residues: 871
  helix:  1.39 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -0.08 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.003   TRP X 207 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.016   0.002   PHE C  25 
 TYR   0.010   0.002   TYR F  98 
 ARG   0.005   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08085 (  862)
  hydrogen bonds       : angle       3.87833 ( 2188)
  covalent geometry    : bond        0.00514 (14927)
  covalent geometry    : angle       0.65956 (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  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9646 (m-80) cc_final: 0.9391 (m-10)
REVERT: B   84 MET cc_start: 0.8996 (tpt) cc_final: 0.8681 (tpp)
REVERT: D   34 TYR cc_start: 0.9479 (m-80) cc_final: 0.9113 (m-80)
REVERT: D   59 MET cc_start: 0.9528 (tpt) cc_final: 0.9095 (tpp)
REVERT: D   62 PHE cc_start: 0.9835 (t80) cc_final: 0.9598 (t80)
REVERT: E  104 PHE cc_start: 0.9461 (m-10) cc_final: 0.9170 (m-80)
REVERT: G  110 ASN cc_start: 0.9101 (t0) cc_final: 0.8700 (p0)
REVERT: H   59 MET cc_start: 0.9697 (mmp) cc_final: 0.9196 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.3184
  time to fit residues: 20.1956
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  : 1.115 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 79 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 106 HIS ** 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 = 0.025387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.019933 restraints weight = 299101.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.020297 restraints weight = 195138.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.020540 restraints weight = 143518.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          1.0097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  14927  Z= 0.287
  Angle     :  0.701   8.821  21596  Z= 0.411
  Chirality :  0.039   0.164   2457
  Planarity :  0.006   0.046   1569
  Dihedral  : 32.959 173.755   4747
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 24.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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:  1.14 (0.27), residues: 871
  helix:  1.12 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.17 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP X 207 
 HIS   0.005   0.001   HIS G  31 
 PHE   0.017   0.002   PHE X 149 
 TYR   0.012   0.002   TYR D 118 
 ARG   0.005   0.001   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09742 (  862)
  hydrogen bonds       : angle       4.16436 ( 2188)
  covalent geometry    : bond        0.00624 (14927)
  covalent geometry    : angle       0.70108 (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
  44 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9565 (m-80) cc_final: 0.9316 (m-80)
REVERT: B   84 MET cc_start: 0.8977 (tpt) cc_final: 0.8677 (tpp)
REVERT: D   34 TYR cc_start: 0.9497 (m-80) cc_final: 0.9157 (m-80)
REVERT: D   59 MET cc_start: 0.9555 (tpt) cc_final: 0.9316 (tpp)
REVERT: E  104 PHE cc_start: 0.9399 (m-10) cc_final: 0.9028 (m-80)
REVERT: G  110 ASN cc_start: 0.9060 (t0) cc_final: 0.8483 (p0)
REVERT: H   59 MET cc_start: 0.9665 (mmp) cc_final: 0.9266 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.3266
  time to fit residues: 20.8858
Evaluate side-chains
  33 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 79 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   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  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 ASN ** 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 = 0.2799 r_free = 0.2799 target = 0.025660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.020108 restraints weight = 289457.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.020558 restraints weight = 173705.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.020857 restraints weight = 120520.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          1.0394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  14927  Z= 0.270
  Angle     :  0.687   8.629  21596  Z= 0.404
  Chirality :  0.039   0.168   2457
  Planarity :  0.005   0.045   1569
  Dihedral  : 32.985 174.630   4747
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 22.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.16 (0.28), residues: 871
  helix:  1.16 (0.19), residues: 655
  sheet:  None (None), residues: 0
  loop : -0.20 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP X 207 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.019   0.002   PHE X 149 
 TYR   0.013   0.002   TYR F  98 
 ARG   0.005   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08993 (  862)
  hydrogen bonds       : angle       4.06131 ( 2188)
  covalent geometry    : bond        0.00585 (14927)
  covalent geometry    : angle       0.68723 (21596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3330.47 seconds
wall clock time: 59 minutes 5.19 seconds (3545.19 seconds total)