Starting phenix.real_space_refine
on Sat Aug 23 17:29:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g88_29843/08_2025/8g88_29843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g88_29843/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2025/8g88_29843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2025/8g88_29843.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2025/8g88_29843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g88_29843/08_2025/8g88_29843.map"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.72, per 1000 atoms: 0.27
  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: 1.06
  Conformation dependent library (CDL) restraints added in 502.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 2.05
  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: 2.84

  Time building geometry restraints manager: 1.58 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.850
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.850
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (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
 ARG   0.004   0.000   ARG H  83 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.011   0.001   PHE X 187 
 TRP   0.022   0.003   TRP X 277 
 HIS   0.003   0.001   HIS B  75 

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

*********************** 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  : 0.207 
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: 0.1407
  time to fit residues: 27.5017
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  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0470
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    4.8086

-------------------------------------------------------------------------------
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
H  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.031299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.025290 restraints weight = 248404.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.025712 restraints weight = 171565.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.026022 restraints weight = 131064.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.026246 restraints weight = 106723.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.026410 restraints weight = 90335.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3542

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= 0.262
  Angle     :  0.683   9.284  21596  Z= 0.401
  Chirality :  0.037   0.181   2457
  Planarity :  0.005   0.046   1569
  Dihedral  : 31.306 176.282   4747
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.27), residues: 871
  helix:  1.99 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -0.11 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  92 
 TYR   0.013   0.002   TYR D  37 
 PHE   0.030   0.002   PHE X 278 
 TRP   0.009   0.002   TRP X 277 
 HIS   0.006   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (14927)
  covalent geometry    : angle       0.68331 (21596)
  hydrogen bonds       : bond        0.08028 (  862)
  hydrogen bonds       : angle       3.45958 ( 2188)

*********************** 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
  82 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.230 
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: A   90 MET cc_start: 0.9679 (mtm) cc_final: 0.9474 (ptp)
REVERT: B   84 MET cc_start: 0.9430 (tpt) cc_final: 0.9084 (tpp)
REVERT: D   59 MET cc_start: 0.9605 (mmp) cc_final: 0.9175 (mmm)
REVERT: E   97 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8717 (mt-10)
REVERT: E  120 MET cc_start: 0.9347 (mtm) cc_final: 0.9131 (mtt)
REVERT: H   59 MET cc_start: 0.9660 (mmp) cc_final: 0.9195 (mmm)
REVERT: H   70 ILE cc_start: 0.9671 (mt) cc_final: 0.9450 (tp)
REVERT: H   97 LEU cc_start: 0.8371 (mt) cc_final: 0.8138 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1301
  time to fit residues: 14.5629
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  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** 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
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.027855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.022071 restraints weight = 271426.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.022472 restraints weight = 185201.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.022735 restraints weight = 139857.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.022956 restraints weight = 114192.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.023052 restraints weight = 96623.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.5848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087  14927  Z= 0.286
  Angle     :  0.697   9.399  21596  Z= 0.408
  Chirality :  0.038   0.181   2457
  Planarity :  0.006   0.044   1569
  Dihedral  : 32.126 175.520   4747
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 20.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.27), residues: 871
  helix:  1.64 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop :  0.34 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  39 
 TYR   0.012   0.002   TYR E  99 
 PHE   0.020   0.002   PHE X 278 
 TRP   0.012   0.002   TRP X 277 
 HIS   0.007   0.002   HIS X 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 (14927)
  covalent geometry    : angle       0.69739 (21596)
  hydrogen bonds       : bond        0.09517 (  862)
  hydrogen bonds       : angle       3.76665 ( 2188)

*********************** 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
  56 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.222 
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: 0.9431 (pt0) cc_final: 0.9150 (pt0)
REVERT: B   84 MET cc_start: 0.9210 (tpt) cc_final: 0.8892 (tpp)
REVERT: D   62 PHE cc_start: 0.9800 (t80) cc_final: 0.9546 (t80)
REVERT: E   86 SER cc_start: 0.9435 (p) cc_final: 0.9173 (p)
REVERT: E   90 MET cc_start: 0.9500 (mmp) cc_final: 0.9256 (ptp)
REVERT: E  104 PHE cc_start: 0.9595 (m-10) cc_final: 0.9266 (m-80)
REVERT: H   59 MET cc_start: 0.9702 (mmp) cc_final: 0.9270 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1319
  time to fit residues: 10.1500
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  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   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  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 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**
** H  92 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 = 0.2823 r_free = 0.2823 target = 0.026699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.021095 restraints weight = 280133.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.021567 restraints weight = 174200.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.021897 restraints weight = 123045.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.022140 restraints weight = 94960.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.022298 restraints weight = 77423.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.7236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  14927  Z= 0.285
  Angle     :  0.692   9.790  21596  Z= 0.405
  Chirality :  0.038   0.155   2457
  Planarity :  0.005   0.054   1569
  Dihedral  : 32.520 172.658   4747
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 21.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.27), residues: 871
  helix:  1.51 (0.19), residues: 651
  sheet:  None (None), residues: 0
  loop :  0.14 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  77 
 TYR   0.014   0.002   TYR H  37 
 PHE   0.012   0.002   PHE X 278 
 TRP   0.011   0.002   TRP X 277 
 HIS   0.005   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (14927)
  covalent geometry    : angle       0.69247 (21596)
  hydrogen bonds       : bond        0.09123 (  862)
  hydrogen bonds       : angle       3.85973 ( 2188)

*********************** 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
  47 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.344 
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: 0.9125 (pt0) cc_final: 0.8846 (pt0)
REVERT: B   84 MET cc_start: 0.9236 (tpt) cc_final: 0.8760 (tpp)
REVERT: D   59 MET cc_start: 0.9341 (tpt) cc_final: 0.8837 (tpp)
REVERT: D   62 PHE cc_start: 0.9703 (t80) cc_final: 0.9442 (t80)
REVERT: E   86 SER cc_start: 0.9416 (p) cc_final: 0.8842 (p)
REVERT: E  104 PHE cc_start: 0.9483 (m-10) cc_final: 0.8963 (m-10)
REVERT: H   59 MET cc_start: 0.9565 (mmp) cc_final: 0.8724 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1265
  time to fit residues: 8.4677
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  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0870
   chunk 57 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 47 optimal weight:   30.0000
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    3.5764

-------------------------------------------------------------------------------
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
** 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**
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.027319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.021696 restraints weight = 270823.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.022172 restraints weight = 165807.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.022524 restraints weight = 115914.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.022745 restraints weight = 88446.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.022913 restraints weight = 72627.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.7529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14927  Z= 0.215
  Angle     :  0.638   9.283  21596  Z= 0.377
  Chirality :  0.036   0.151   2457
  Planarity :  0.004   0.045   1569
  Dihedral  : 32.211 172.956   4747
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 17.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.28), residues: 871
  helix:  1.68 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop :  0.12 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  89 
 TYR   0.025   0.002   TYR C  50 
 PHE   0.019   0.002   PHE B  61 
 TRP   0.008   0.002   TRP X 277 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (14927)
  covalent geometry    : angle       0.63782 (21596)
  hydrogen bonds       : bond        0.06731 (  862)
  hydrogen bonds       : angle       3.65583 ( 2188)

*********************** 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
  43 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9201 (tpt) cc_final: 0.8919 (tpp)
REVERT: D   59 MET cc_start: 0.9483 (tpt) cc_final: 0.9090 (tpp)
REVERT: D   62 PHE cc_start: 0.9769 (t80) cc_final: 0.9501 (t80)
REVERT: E  104 PHE cc_start: 0.9516 (m-10) cc_final: 0.9162 (m-10)
REVERT: E  120 MET cc_start: 0.9252 (mtm) cc_final: 0.8925 (mtt)
REVERT: H   59 MET cc_start: 0.9688 (mmp) cc_final: 0.9301 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1204
  time to fit residues: 7.2376
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  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:   40.0000
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 91 optimal weight:   10.0000
   overall best weight:    4.7386

-------------------------------------------------------------------------------
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**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 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 = 0.2834 r_free = 0.2834 target = 0.026772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.021011 restraints weight = 280801.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.021492 restraints weight = 171700.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.021825 restraints weight = 120811.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022043 restraints weight = 93215.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.022176 restraints weight = 76592.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.8264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  14927  Z= 0.259
  Angle     :  0.663   9.028  21596  Z= 0.390
  Chirality :  0.037   0.159   2457
  Planarity :  0.005   0.044   1569
  Dihedral  : 32.472 173.444   4747
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 21.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.33 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.28), residues: 871
  helix:  1.54 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.05 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  42 
 TYR   0.014   0.002   TYR C  50 
 PHE   0.018   0.002   PHE C  25 
 TRP   0.007   0.002   TRP X 277 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (14927)
  covalent geometry    : angle       0.66322 (21596)
  hydrogen bonds       : bond        0.08766 (  862)
  hydrogen bonds       : angle       3.79083 ( 2188)

*********************** 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
  42 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9188 (tpt) cc_final: 0.8846 (tpp)
REVERT: E  104 PHE cc_start: 0.9504 (m-10) cc_final: 0.9201 (m-10)
REVERT: H   59 MET cc_start: 0.9688 (mmp) cc_final: 0.9294 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1306
  time to fit residues: 7.6915
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  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 36 optimal weight:   30.0000
   chunk 16 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 91 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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  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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.025379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2511 r_free = 0.2511 target = 0.019478 restraints weight = 299356.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2532 r_free = 0.2532 target = 0.019926 restraints weight = 186432.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.020226 restraints weight = 131899.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.020426 restraints weight = 101978.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.020605 restraints weight = 84367.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.9635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.095  14927  Z= 0.358
  Angle     :  0.773  10.444  21596  Z= 0.448
  Chirality :  0.043   0.200   2457
  Planarity :  0.006   0.062   1569
  Dihedral  : 33.327 174.245   4747
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 31.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.27), residues: 871
  helix:  0.90 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.41 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  77 
 TYR   0.018   0.002   TYR D 118 
 PHE   0.035   0.003   PHE C  25 
 TRP   0.008   0.002   TRP X 207 
 HIS   0.005   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00787 (14927)
  covalent geometry    : angle       0.77280 (21596)
  hydrogen bonds       : bond        0.12571 (  862)
  hydrogen bonds       : angle       4.33788 ( 2188)

*********************** 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
  41 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9327 (m-10) cc_final: 0.9023 (m-10)
REVERT: B   84 MET cc_start: 0.8935 (tpt) cc_final: 0.8258 (tpp)
REVERT: D   34 TYR cc_start: 0.9312 (m-80) cc_final: 0.8937 (m-80)
REVERT: D   59 MET cc_start: 0.9347 (tpt) cc_final: 0.8968 (tpp)
REVERT: D   62 PHE cc_start: 0.9711 (t80) cc_final: 0.9338 (t80)
REVERT: E   86 SER cc_start: 0.9490 (p) cc_final: 0.9050 (p)
REVERT: E   90 MET cc_start: 0.9278 (mmp) cc_final: 0.8983 (ptp)
REVERT: E  104 PHE cc_start: 0.9536 (m-10) cc_final: 0.8988 (m-80)
REVERT: H   59 MET cc_start: 0.9677 (mmp) cc_final: 0.8889 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1371
  time to fit residues: 7.9701
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  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 ASN ** 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 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.025216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2518 r_free = 0.2518 target = 0.019745 restraints weight = 302555.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.020109 restraints weight = 200490.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2544 r_free = 0.2544 target = 0.020359 restraints weight = 148879.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.020530 restraints weight = 119915.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.020656 restraints weight = 102614.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.9938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080  14927  Z= 0.320
  Angle     :  0.732   9.532  21596  Z= 0.428
  Chirality :  0.040   0.171   2457
  Planarity :  0.006   0.056   1569
  Dihedral  : 33.288 173.190   4747
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 26.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.27), residues: 871
  helix:  0.94 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.44 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  89 
 TYR   0.014   0.002   TYR F  98 
 PHE   0.021   0.002   PHE A  67 
 TRP   0.007   0.002   TRP X 207 
 HIS   0.005   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (14927)
  covalent geometry    : angle       0.73239 (21596)
  hydrogen bonds       : bond        0.10683 (  862)
  hydrogen bonds       : angle       4.22766 ( 2188)

*********************** 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
  41 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8970 (tpt) cc_final: 0.8590 (tpp)
REVERT: D   34 TYR cc_start: 0.9513 (m-80) cc_final: 0.9224 (m-80)
REVERT: D   59 MET cc_start: 0.9564 (tpt) cc_final: 0.9276 (tpp)
REVERT: E  104 PHE cc_start: 0.9431 (m-10) cc_final: 0.9060 (m-80)
REVERT: H   59 MET cc_start: 0.9711 (mmp) cc_final: 0.9214 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1207
  time to fit residues: 7.3795
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  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 70 optimal weight:   20.0000
   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  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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.025492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.019979 restraints weight = 299311.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.020361 restraints weight = 193603.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.020630 restraints weight = 141233.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.020804 restraints weight = 112190.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.020954 restraints weight = 95520.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          1.0072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  14927  Z= 0.262
  Angle     :  0.698   9.471  21596  Z= 0.408
  Chirality :  0.039   0.191   2457
  Planarity :  0.005   0.047   1569
  Dihedral  : 33.109 173.564   4747
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 22.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.27), residues: 871
  helix:  1.02 (0.19), residues: 655
  sheet:  None (None), residues: 0
  loop : -0.39 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  89 
 TYR   0.010   0.002   TYR D  37 
 PHE   0.021   0.002   PHE D  62 
 TRP   0.011   0.002   TRP X 207 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (14927)
  covalent geometry    : angle       0.69769 (21596)
  hydrogen bonds       : bond        0.08645 (  862)
  hydrogen bonds       : angle       4.08497 ( 2188)

*********************** 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  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9004 (tpt) cc_final: 0.8745 (tpp)
REVERT: D   34 TYR cc_start: 0.9470 (m-80) cc_final: 0.9148 (m-80)
REVERT: D   59 MET cc_start: 0.9553 (tpt) cc_final: 0.9103 (tpp)
REVERT: D   62 PHE cc_start: 0.9802 (t80) cc_final: 0.9592 (t80)
REVERT: E  104 PHE cc_start: 0.9437 (m-10) cc_final: 0.9074 (m-80)
REVERT: H   59 MET cc_start: 0.9660 (mmp) cc_final: 0.9228 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1236
  time to fit residues: 7.5784
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  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 88 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 ASN ** 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  81 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 = 0.2760 r_free = 0.2760 target = 0.024731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2507 r_free = 0.2507 target = 0.019314 restraints weight = 304216.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.019705 restraints weight = 195646.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.019957 restraints weight = 142626.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2541 r_free = 0.2541 target = 0.020130 restraints weight = 113249.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.020213 restraints weight = 95409.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.2457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          1.0561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.095  14927  Z= 0.334
  Angle     :  0.753  11.901  21596  Z= 0.437
  Chirality :  0.042   0.224   2457
  Planarity :  0.006   0.081   1569
  Dihedral  : 33.542 174.579   4747
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 29.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 871
  helix:  0.82 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.68 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  42 
 TYR   0.014   0.002   TYR F  98 
 PHE   0.021   0.002   PHE A  67 
 TRP   0.010   0.002   TRP X 207 
 HIS   0.006   0.002   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 (14927)
  covalent geometry    : angle       0.75340 (21596)
  hydrogen bonds       : bond        0.11788 (  862)
  hydrogen bonds       : angle       4.30646 ( 2188)

********************** 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
  42 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9579 (m-10) cc_final: 0.9346 (m-10)
REVERT: B   84 MET cc_start: 0.8984 (tpt) cc_final: 0.8724 (tpp)
REVERT: C  110 ASN cc_start: 0.9064 (t0) cc_final: 0.8627 (p0)
REVERT: D   34 TYR cc_start: 0.9471 (m-80) cc_final: 0.9176 (m-80)
REVERT: E  104 PHE cc_start: 0.9416 (m-10) cc_final: 0.9061 (m-80)
REVERT: H   59 MET cc_start: 0.9643 (mmp) cc_final: 0.9240 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1212
  time to fit residues: 7.3812
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  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 84 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 94 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    4.1586

-------------------------------------------------------------------------------
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  75 HIS ** 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**
** H  81 ASN ** 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 = 0.2777 r_free = 0.2777 target = 0.025513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.019988 restraints weight = 296265.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.020390 restraints weight = 187905.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.020658 restraints weight = 135647.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.020819 restraints weight = 107084.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.020885 restraints weight = 91190.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.2484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          1.0491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  14927  Z= 0.236
  Angle     :  0.689  10.431  21596  Z= 0.401
  Chirality :  0.038   0.176   2457
  Planarity :  0.005   0.048   1569
  Dihedral  : 33.230 173.854   4747
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 21.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.27), residues: 871
  helix:  0.98 (0.19), residues: 654
  sheet:  None (None), residues: 0
  loop : -0.60 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  69 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.013   0.002   PHE A  67 
 TRP   0.005   0.002   TRP X 277 
 HIS   0.005   0.002   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (14927)
  covalent geometry    : angle       0.68942 (21596)
  hydrogen bonds       : bond        0.07974 (  862)
  hydrogen bonds       : angle       4.04269 ( 2188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1466.64 seconds
wall clock time: 26 minutes 18.80 seconds (1578.80 seconds total)