Starting phenix.real_space_refine
on Wed Sep 17 15:33:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k9l_62193/09_2025/9k9l_62193.cif"
  }
  resolution = 3.66
  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=   0.006
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     242      5.49       5
     S       8      5.16       5
     C    5446      2.51       5
     N    1855      2.21       5
     O    2262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9813
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 621
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 628
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 634
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 2, 'TRANS': 75}
    Chain: "F"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "G"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 621
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 2.42, per 1000 atoms: 0.25
  Number of scatterers: 9813
  At special positions: 0
  Unit cell: (111.3, 118.72, 100.7, 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       8     16.00
     P     242     15.00
     O    2262      8.00
     N    1855      7.00
     C    5446      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: 0.96
  Conformation dependent library (CDL) restraints added in 201.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      79.8% alpha, 2.3% beta
      120 base pairs and 184 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 80
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 122 through 134
      removed outlier: 3.781A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.517A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    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 94
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.532A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 116
    Processing helix  chain 'C' and resid 122 through 134
      removed outlier: 3.869A  pdb=" N   VAL C 126 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN C 127 " --> pdb=" O   PRO C 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 29
      removed outlier: 3.551A  pdb=" N   ILE D  29 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'E' and resid 63 through 80
      removed outlier: 3.504A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   THR E  79 " --> pdb=" O   CYS E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.502A  pdb=" N   ALA E 116 " --> pdb=" O   LEU E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.553A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA E 129 " --> pdb=" O   ASP E 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.628A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 116
    Processing helix  chain 'G' and resid 122 through 134
    Processing helix  chain 'H' and resid 24 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.877A  pdb=" N   ASN A  85 " --> 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 120 through 121
      removed outlier: 3.705A  pdb=" N   LEU A 121 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86
      removed outlier: 6.652A  pdb=" N   ASN C  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.763A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA6, first strand: chain 'G' and resid 85 through 86
      removed outlier: 6.801A  pdb=" N   ASN G  85 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 120 through 121

    360 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      312 hydrogen bonds
      624 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      184 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1883
        1.33 -     1.45: 3461
        1.45 -     1.57: 4650
        1.57 -     1.69: 482
        1.69 -     1.81: 12
  Bond restraints: 10488
  Sorted by residual:
  bond pdb=" N   VAL D  81 "
       pdb=" CA  VAL D  81 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.033 1.10e-02 8.26e+03 9.25e+00
  bond pdb=" N   ARG D  78 "
       pdb=" CA  ARG D  78 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.33e-02 5.65e+03 5.65e+00
  bond pdb=" N   LYS D  79 "
       pdb=" CA  LYS D  79 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.22e-02 6.72e+03 5.54e+00
  bond pdb=" N   GLU D  74 "
       pdb=" CA  GLU D  74 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.47e+00
  bond pdb=" N   HIS D  75 "
       pdb=" CA  HIS D  75 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.46e+00
  ... (remaining 10483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 14548
        1.46 -     2.91: 579
        2.91 -     4.37: 49
        4.37 -     5.82: 24
        5.82 -     7.28: 3
  Bond angle restraints: 15203
  Sorted by residual:
  angle pdb=" CA  LYS D  77 "
        pdb=" C   LYS D  77 "
        pdb=" O   LYS D  77 "
      ideal   model   delta    sigma   weight residual
     121.84  118.24    3.60 1.16e+00 7.43e-01 9.61e+00
  angle pdb=" N   ALA D  76 "
        pdb=" CA  ALA D  76 "
        pdb=" C   ALA D  76 "
      ideal   model   delta    sigma   weight residual
     113.20  109.47    3.73 1.21e+00 6.83e-01 9.52e+00
  angle pdb=" CA  THR D  80 "
        pdb=" CB  THR D  80 "
        pdb=" OG1 THR D  80 "
      ideal   model   delta    sigma   weight residual
     109.60  104.99    4.61 1.50e+00 4.44e-01 9.46e+00
  angle pdb=" CA  THR D  73 "
        pdb=" CB  THR D  73 "
        pdb=" OG1 THR D  73 "
      ideal   model   delta    sigma   weight residual
     109.60  105.13    4.47 1.50e+00 4.44e-01 8.88e+00
  angle pdb=" CA  ARG D  78 "
        pdb=" C   ARG D  78 "
        pdb=" O   ARG D  78 "
      ideal   model   delta    sigma   weight residual
     121.58  118.31    3.27 1.16e+00 7.43e-01 7.94e+00
  ... (remaining 15198 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.92: 4356
       32.92 -    65.83: 1211
       65.83 -    98.75: 35
       98.75 -   131.67: 1
      131.67 -   164.58: 3
  Dihedral angle restraints: 5606
    sinusoidal: 3873
      harmonic: 1733
  Sorted by residual:
  dihedral pdb=" C4'  DC I  51 "
           pdb=" C3'  DC I  51 "
           pdb=" O3'  DC I  51 "
           pdb=" P    DA I  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   55.42  164.58     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DT I  14 "
           pdb=" C3'  DT I  14 "
           pdb=" O3'  DT I  14 "
           pdb=" P    DT I  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   59.11  160.89     1      3.50e+01 8.16e-04 1.52e+01
  dihedral pdb=" C4'  DC I -48 "
           pdb=" C3'  DC I -48 "
           pdb=" O3'  DC I -48 "
           pdb=" P    DG I -47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.50  155.50     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 5603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 1714
       0.109 -    0.217: 17
       0.217 -    0.326: 1
       0.326 -    0.434: 0
       0.434 -    0.543: 1
  Chirality restraints: 1733
  Sorted by residual:
  chirality pdb=" P    DC I  51 "
            pdb=" OP1  DC I  51 "
            pdb=" OP2  DC I  51 "
            pdb=" O5'  DC I  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.54 2.00e-01 2.50e+01 7.37e+00
  chirality pdb=" CB  ILE H  46 "
            pdb=" CA  ILE H  46 "
            pdb=" CG1 ILE H  46 "
            pdb=" CG2 ILE H  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  ILE H  26 "
            pdb=" CA  ILE H  26 "
            pdb=" CG1 ILE H  26 "
            pdb=" CG2 ILE H  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1730 not shown)

  Planarity restraints: 1077
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 107 "    0.014 2.00e-02 2.50e+03   2.83e-02 8.00e+00
        pdb=" C   GLU C 107 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU C 107 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASP C 108 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  78 "    0.241 9.50e-02 1.11e+02   1.08e-01 7.15e+00
        pdb=" NE  ARG D  78 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  78 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  50 "    0.012 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" C   ILE B  50 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE B  50 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR B  51 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1074 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1756
        2.78 -     3.31: 9056
        3.31 -     3.84: 19758
        3.84 -     4.37: 22053
        4.37 -     4.90: 31413
  Nonbonded interactions: 84036
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  63 "
            pdb=" NZ  LYS F  91 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OG  SER C  68 "
            pdb=" NH2 ARG C  72 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   LEU C  61 "
            pdb=" NH2 ARG D  36 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" NH2 ARG G  72 "
            pdb=" OP1  DC I   8 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" N   VAL A 119 "
            pdb=" OP1  DC J  28 "
     model   vdw
     2.325 3.120
  ... (remaining 84031 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'
  selection = (chain 'C' and resid 59 through 134)
  selection = (chain 'E' and resid 59 through 134)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  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=1.00 max=1.00 mean=1.00
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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.540
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
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   0.057  10488  Z= 0.198
  Angle     :  0.655   7.280  15203  Z= 0.411
  Chirality :  0.039   0.543   1733
  Planarity :  0.006   0.108   1077
  Dihedral  : 28.694 164.584   4480
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  4.41 %
    Favored  : 94.79 %
  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:  0.22 (0.29), residues: 583
  helix:  0.48 (0.20), residues: 473
  sheet:  None (None), residues: 0
  loop : -0.88 (0.43), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 130 
 TYR   0.018   0.002   TYR D  88 
 PHE   0.018   0.002   PHE E 106 
 TRP   0.003   0.001   TRP C  86 
 HIS   0.002   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (10488)
  covalent geometry    : angle       0.65478 (15203)
  hydrogen bonds       : bond        0.10569 (  672)
  hydrogen bonds       : angle       3.60412 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: E   78 PHE cc_start: 0.7743 (m-80) cc_final: 0.7333 (m-80)
REVERT: E   85 ASN cc_start: 0.8309 (m-40) cc_final: 0.8053 (m-40)
REVERT: G   80 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7045 (ptp90)
REVERT: H   91 LYS cc_start: 0.7721 (tttt) cc_final: 0.7345 (mttt)
REVERT: H   93 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7269 (tm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2425
  time to fit residues: 23.6786
Evaluate side-chains
  57 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
C  85 ASN
D  27 GLN
E 115 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.215550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.154472 restraints weight = 11702.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.151804 restraints weight = 19672.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153811 restraints weight = 14977.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154649 restraints weight = 11128.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.155470 restraints weight = 10743.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10488  Z= 0.166
  Angle     :  0.575   5.503  15203  Z= 0.341
  Chirality :  0.034   0.146   1733
  Planarity :  0.004   0.034   1077
  Dihedral  : 31.930 171.612   3289
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.02 %
    Favored  : 89.38 %
  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:  2.59 (0.32), residues: 583
  helix:  2.45 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -1.23 (0.39), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  40 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.015   0.001   PHE E  67 
 TRP   0.004   0.001   TRP G  86 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10488)
  covalent geometry    : angle       0.57530 (15203)
  hydrogen bonds       : bond        0.04520 (  672)
  hydrogen bonds       : angle       2.81985 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7186 (ttm-80)
REVERT: C   77 LYS cc_start: 0.8335 (mttp) cc_final: 0.8102 (mttp)
REVERT: D   50 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8058 (tp)
REVERT: E   85 ASN cc_start: 0.8180 (m-40) cc_final: 0.7923 (m-40)
REVERT: F   92 ARG cc_start: 0.7335 (ttp80) cc_final: 0.7065 (ttm-80)
REVERT: H   91 LYS cc_start: 0.8061 (tttt) cc_final: 0.7694 (ttmt)
  outliers start: 8
  outliers final: 4
  residues processed: 67
  average time/residue: 0.1771
  time to fit residues: 14.7621
Evaluate side-chains
  58 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 49 optimal weight:    0.4980
   chunk 64 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
** H  75 HIS ** 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 = 0.4333 r_free = 0.4333 target = 0.210784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.150019 restraints weight = 11833.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.151048 restraints weight = 22947.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.152157 restraints weight = 20299.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.152340 restraints weight = 14254.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.152704 restraints weight = 14375.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10488  Z= 0.152
  Angle     :  0.537   4.817  15203  Z= 0.321
  Chirality :  0.033   0.130   1733
  Planarity :  0.003   0.033   1077
  Dihedral  : 31.892 171.264   3289
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.22 %
    Favored  : 87.37 %
  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:  3.28 (0.33), residues: 583
  helix:  2.92 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -0.87 (0.40), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  40 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.013   0.002   TRP C  86 
 HIS   0.001   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (10488)
  covalent geometry    : angle       0.53671 (15203)
  hydrogen bonds       : bond        0.04228 (  672)
  hydrogen bonds       : angle       2.63369 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.9048 (m-80) cc_final: 0.8800 (m-80)
REVERT: B   92 ARG cc_start: 0.7637 (ttp80) cc_final: 0.6938 (ttm-80)
  outliers start: 7
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1973
  time to fit residues: 17.9272
Evaluate side-chains
  58 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 79 optimal weight:   10.0000
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
E  85 ASN
** H  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.196115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139462 restraints weight = 12031.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.137442 restraints weight = 23551.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.138878 restraints weight = 18434.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.140141 restraints weight = 13366.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140834 restraints weight = 12143.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  10488  Z= 0.243
  Angle     :  0.653   6.634  15203  Z= 0.377
  Chirality :  0.038   0.173   1733
  Planarity :  0.005   0.069   1077
  Dihedral  : 32.559 177.538   3289
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 11.62 %
    Favored  : 84.57 %
  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:  2.47 (0.33), residues: 583
  helix:  2.34 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.15 (0.43), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  40 
 TYR   0.028   0.002   TYR F  88 
 PHE   0.013   0.002   PHE A  67 
 TRP   0.016   0.002   TRP C  86 
 HIS   0.005   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 (10488)
  covalent geometry    : angle       0.65331 (15203)
  hydrogen bonds       : bond        0.05736 (  672)
  hydrogen bonds       : angle       3.05183 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.236 
Fit side-chains
REVERT: D   50 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8137 (tp)
REVERT: E  121 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8731 (tt)
REVERT: E  122 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8541 (m-80)
REVERT: F   72 TYR cc_start: 0.7666 (m-10) cc_final: 0.7339 (m-80)
REVERT: F   77 LYS cc_start: 0.7260 (mmmt) cc_final: 0.6946 (mmtp)
  outliers start: 19
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1509
  time to fit residues: 15.1149
Evaluate side-chains
  67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   79 THR
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 58 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.207323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.146398 restraints weight = 11745.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.146475 restraints weight = 23252.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.147928 restraints weight = 21326.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.148238 restraints weight = 15544.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.148689 restraints weight = 15892.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10488  Z= 0.156
  Angle     :  0.548   8.053  15203  Z= 0.327
  Chirality :  0.033   0.137   1733
  Planarity :  0.004   0.035   1077
  Dihedral  : 32.254 177.270   3289
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.43 %
    Favored  : 83.57 %
  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:  3.03 (0.33), residues: 583
  helix:  2.76 (0.23), residues: 458
  sheet:  None (None), residues: 0
  loop : -1.05 (0.42), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  78 
 TYR   0.013   0.001   TYR F  88 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.012   0.001   TRP C  86 
 HIS   0.001   0.000   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10488)
  covalent geometry    : angle       0.54753 (15203)
  hydrogen bonds       : bond        0.04244 (  672)
  hydrogen bonds       : angle       2.65768 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.250 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7261 (ttm-80)
REVERT: E  122 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8215 (m-80)
REVERT: F   77 LYS cc_start: 0.7234 (mmmt) cc_final: 0.7023 (mmtp)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1474
  time to fit residues: 13.4012
Evaluate side-chains
  61 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 68 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
G  95 GLN
** H  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.193132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.136856 restraints weight = 11892.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.134923 restraints weight = 26604.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.137128 restraints weight = 20129.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.139602 restraints weight = 13568.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.140224 restraints weight = 12020.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074  10488  Z= 0.331
  Angle     :  0.734   8.650  15203  Z= 0.416
  Chirality :  0.041   0.171   1733
  Planarity :  0.005   0.063   1077
  Dihedral  : 33.006 176.381   3289
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 13.63 %
    Favored  : 82.77 %
  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:  1.91 (0.33), residues: 583
  helix:  1.95 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.39 (0.42), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  67 
 TYR   0.034   0.003   TYR F  88 
 PHE   0.015   0.003   PHE E  78 
 TRP   0.011   0.002   TRP E  86 
 HIS   0.003   0.001   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00800 (10488)
  covalent geometry    : angle       0.73363 (15203)
  hydrogen bonds       : bond        0.06279 (  672)
  hydrogen bonds       : angle       3.12383 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7604 (ttp-170)
REVERT: D   44 LYS cc_start: 0.5887 (mtpp) cc_final: 0.5313 (mmmt)
REVERT: E  122 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8559 (m-80)
REVERT: F   77 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6894 (mmtp)
  outliers start: 18
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1678
  time to fit residues: 14.6623
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 57 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
** H  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.198315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.139392 restraints weight = 11685.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.138662 restraints weight = 23451.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.140152 restraints weight = 19083.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.141150 restraints weight = 13812.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.141989 restraints weight = 12758.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10488  Z= 0.199
  Angle     :  0.596   7.776  15203  Z= 0.350
  Chirality :  0.035   0.136   1733
  Planarity :  0.004   0.037   1077
  Dihedral  : 32.721 178.554   3289
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 14.03 %
    Favored  : 82.36 %
  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:  2.49 (0.33), residues: 583
  helix:  2.39 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.35 (0.42), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 130 
 TYR   0.016   0.002   TYR F  88 
 PHE   0.010   0.001   PHE E  78 
 TRP   0.010   0.001   TRP C  86 
 HIS   0.002   0.001   HIS G 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (10488)
  covalent geometry    : angle       0.59559 (15203)
  hydrogen bonds       : bond        0.04786 (  672)
  hydrogen bonds       : angle       2.76915 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.262 
Fit side-chains
REVERT: D   44 LYS cc_start: 0.5930 (mtpp) cc_final: 0.5294 (mmmt)
REVERT: E  122 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8402 (m-80)
REVERT: F   77 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6916 (mmtp)
REVERT: H   93 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8028 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 68
  average time/residue: 0.1537
  time to fit residues: 13.4788
Evaluate side-chains
  66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
** H  75 HIS ** 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 = 0.4104 r_free = 0.4104 target = 0.188601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.131870 restraints weight = 11788.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.134899 restraints weight = 28008.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.136117 restraints weight = 17136.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136579 restraints weight = 12713.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.137307 restraints weight = 11801.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10488  Z= 0.238
  Angle     :  0.637   7.115  15203  Z= 0.370
  Chirality :  0.037   0.154   1733
  Planarity :  0.004   0.053   1077
  Dihedral  : 32.868 179.038   3289
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.83 %
    Favored  : 81.96 %
  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:  2.27 (0.33), residues: 583
  helix:  2.23 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.38 (0.44), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 118 
 TYR   0.023   0.002   TYR F  88 
 PHE   0.012   0.002   PHE A  67 
 TRP   0.011   0.002   TRP C  86 
 HIS   0.003   0.001   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (10488)
  covalent geometry    : angle       0.63731 (15203)
  hydrogen bonds       : bond        0.05356 (  672)
  hydrogen bonds       : angle       2.87946 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7309 (ttm170)
REVERT: E  122 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8465 (m-80)
REVERT: F   77 LYS cc_start: 0.7112 (mmmt) cc_final: 0.6896 (mmtp)
REVERT: H   93 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8018 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 67
  average time/residue: 0.1511
  time to fit residues: 13.0337
Evaluate side-chains
  66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0980
   chunk 76 optimal weight:    6.9990
   chunk 67 optimal weight:    8.9990
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.196142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.137701 restraints weight = 11720.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.137104 restraints weight = 21995.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.138500 restraints weight = 18935.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138950 restraints weight = 14000.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.139780 restraints weight = 13839.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.5749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10488  Z= 0.149
  Angle     :  0.544   6.780  15203  Z= 0.326
  Chirality :  0.033   0.129   1733
  Planarity :  0.003   0.037   1077
  Dihedral  : 32.463 178.917   3289
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.03 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.33), residues: 583
  helix:  2.72 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.35 (0.43), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  39 
 TYR   0.012   0.001   TYR H  88 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.011   0.001   TRP C  86 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10488)
  covalent geometry    : angle       0.54384 (15203)
  hydrogen bonds       : bond        0.04161 (  672)
  hydrogen bonds       : angle       2.55057 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.7149 (ttm-80)
REVERT: E  122 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (m-80)
REVERT: H   93 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7917 (tm-30)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1686
  time to fit residues: 14.4760
Evaluate side-chains
  64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 20 optimal weight:    0.4980
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.195576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138463 restraints weight = 11537.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138659 restraints weight = 22605.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139888 restraints weight = 18389.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.140223 restraints weight = 13494.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.140708 restraints weight = 13606.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.5830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10488  Z= 0.155
  Angle     :  0.553   7.546  15203  Z= 0.327
  Chirality :  0.033   0.126   1733
  Planarity :  0.004   0.054   1077
  Dihedral  : 32.392 178.784   3289
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.04 %
    Favored  : 79.96 %
  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:  3.07 (0.33), residues: 583
  helix:  2.84 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.30 (0.44), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  35 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.009   0.001   PHE A  78 
 TRP   0.009   0.001   TRP C  86 
 HIS   0.002   0.000   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10488)
  covalent geometry    : angle       0.55254 (15203)
  hydrogen bonds       : bond        0.04325 (  672)
  hydrogen bonds       : angle       2.56907 ( 1674)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.7485 (ttp-170) cc_final: 0.6932 (ttm-80)
REVERT: C   72 ARG cc_start: 0.7795 (mtt90) cc_final: 0.6735 (mtt180)
REVERT: E  122 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8345 (m-80)
REVERT: H   93 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7993 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1485
  time to fit residues: 12.7466
Evaluate side-chains
  64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain E residue  122 PHE
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   50 ILE
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 0 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D  27 GLN
** H  75 HIS ** 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 = 0.4180 r_free = 0.4180 target = 0.196080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138930 restraints weight = 11715.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138413 restraints weight = 23784.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.140030 restraints weight = 19266.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.140829 restraints weight = 13915.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141626 restraints weight = 13502.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.5958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10488  Z= 0.154
  Angle     :  0.543   7.101  15203  Z= 0.323
  Chirality :  0.033   0.142   1733
  Planarity :  0.004   0.036   1077
  Dihedral  : 32.239 179.290   3289
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.04 %
    Favored  : 79.96 %
  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:  3.16 (0.33), residues: 583
  helix:  2.89 (0.23), residues: 459
  sheet:  None (None), residues: 0
  loop : -1.24 (0.45), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  72 
 TYR   0.012   0.001   TYR D  88 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.008   0.001   TRP C  86 
 HIS   0.001   0.000   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10488)
  covalent geometry    : angle       0.54336 (15203)
  hydrogen bonds       : bond        0.04321 (  672)
  hydrogen bonds       : angle       2.55102 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1399.05 seconds
wall clock time: 24 minutes 56.29 seconds (1496.29 seconds total)