Starting phenix.real_space_refine
on Thu Feb 13 14:39:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gxa_51645/02_2025/9gxa_51645.cif"
  }
  resolution = 4.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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     224      5.49       5
     S       8      5.16       5
     C    5167      2.51       5
     N    1696      2.21       5
     O    2120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9215
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 575
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 2, 'TRANS': 68}
    Chain: "B"
      Number of atoms: 516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 516
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 1, 'TRANS': 63}
    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: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "E"
      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: "F"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 565
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    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: 541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 541
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 1, 'TRANS': 66}
    Chain: "I"
      Number of atoms: 2292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2292
          Classifications: {'DNA': 112}
          Link IDs: {'rna3p': 111}
    Chain: "J"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2300
          Classifications: {'DNA': 112}
          Link IDs: {'rna3p': 111}
  Time building chain proxies: 6.43, per 1000 atoms: 0.70
  Number of scatterers: 9215
  At special positions: 0
  Unit cell: (86.92, 113.16, 121.36, 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     224     15.00
     O    2120      8.00
     N    1696      7.00
     C    5167      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 656.5 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      78.7% alpha, 0.7% beta
      108 base pairs and 196 stacking pairs defined.
    Time for finding SS restraints: 4.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 4.386A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ILE A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   CYS A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 117
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 4.191A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.520A  pdb=" N   VAL B  86 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  90 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.505A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 116
      removed outlier: 3.548A  pdb=" N   LEU C  92 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 134
      removed outlier: 3.649A  pdb=" N   VAL C 126 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 4.272A  pdb=" N   GLU D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.581A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.726A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.622A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.585A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.708A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 63 through 77
      removed outlier: 3.733A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 117
    Processing helix  chain 'G' and resid 122 through 134
      removed outlier: 3.729A  pdb=" N   VAL G 126 " --> pdb=" O   PHE G 122 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
      removed outlier: 3.807A  pdb=" N   GLY H  28 " --> pdb=" O   ASN H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 41
      removed outlier: 3.578A  pdb=" N   ILE H  34 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 49 through 76
      removed outlier: 4.219A  pdb=" N   GLU H  53 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA H  76 " --> pdb=" O   TYR H  72 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 91
      removed outlier: 3.519A  pdb=" N   VAL H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS H  91 " --> pdb=" O   VAL H  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.361A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'E' and resid 120 through 121

    323 hydrogen bonds defined for protein.
    954 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      258 hydrogen bonds
      516 hydrogen bond angles
      0 basepair planarities
      108 basepair parallelities
      196 stacking parallelities
  Total time for adding SS restraints: 3.56

  Time building geometry restraints manager: 2.98 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: 1867
        1.33 -     1.45: 3149
        1.45 -     1.57: 4370
        1.57 -     1.69: 446
        1.69 -     1.81: 12
  Bond restraints: 9844
  Sorted by residual:
  bond pdb=" N   THR C 120 "
       pdb=" CA  THR C 120 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.31e-02 5.83e+03 9.75e+00
  bond pdb=" N   VAL C 119 "
       pdb=" CA  VAL C 119 "
    ideal  model  delta    sigma   weight residual
    1.460  1.499 -0.039 1.32e-02 5.74e+03 8.84e+00
  bond pdb=" N   VAL E  82 "
       pdb=" CA  VAL E  82 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.22e-02 6.72e+03 8.77e+00
  bond pdb=" N   THR E  79 "
       pdb=" CA  THR E  79 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.19e-02 7.06e+03 8.73e+00
  bond pdb=" N   ARG C 118 "
       pdb=" CA  ARG C 118 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.31e-02 5.83e+03 8.38e+00
  ... (remaining 9839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 13533
        1.39 -     2.77: 660
        2.77 -     4.16: 55
        4.16 -     5.55: 14
        5.55 -     6.93: 3
  Bond angle restraints: 14265
  Sorted by residual:
  angle pdb=" CA  ASP E  83 "
        pdb=" C   ASP E  83 "
        pdb=" O   ASP E  83 "
      ideal   model   delta    sigma   weight residual
     122.27  117.86    4.41 1.16e+00 7.43e-01 1.44e+01
  angle pdb=" CA  PHE C 122 "
        pdb=" C   PHE C 122 "
        pdb=" N   PRO C 123 "
      ideal   model   delta    sigma   weight residual
     117.67  121.35   -3.68 1.01e+00 9.80e-01 1.32e+01
  angle pdb=" CA  ARG C 118 "
        pdb=" C   ARG C 118 "
        pdb=" O   ARG C 118 "
      ideal   model   delta    sigma   weight residual
     120.96  117.08    3.88 1.09e+00 8.42e-01 1.27e+01
  angle pdb=" N   VAL A 119 "
        pdb=" CA  VAL A 119 "
        pdb=" C   VAL A 119 "
      ideal   model   delta    sigma   weight residual
     112.96  109.63    3.33 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" CA  VAL C 119 "
        pdb=" C   VAL C 119 "
        pdb=" O   VAL C 119 "
      ideal   model   delta    sigma   weight residual
     120.46  117.08    3.38 1.11e+00 8.12e-01 9.25e+00
  ... (remaining 14260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 4220
       35.61 -    71.23: 1110
       71.23 -   106.84: 21
      106.84 -   142.46: 2
      142.46 -   178.07: 2
  Dihedral angle restraints: 5355
    sinusoidal: 3693
      harmonic: 1662
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DA J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.07 -178.07     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I  57 "
           pdb=" C3'  DA I  57 "
           pdb=" O3'  DA I  57 "
           pdb=" P    DT I  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.59  175.41     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J  44 "
           pdb=" C3'  DT J  44 "
           pdb=" O3'  DT J  44 "
           pdb=" P    DT J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   -0.19 -139.81     1      3.50e+01 8.16e-04 1.38e+01
  ... (remaining 5352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1317
       0.041 -    0.083: 256
       0.083 -    0.124: 54
       0.124 -    0.165: 6
       0.165 -    0.207: 3
  Chirality restraints: 1636
  Sorted by residual:
  chirality pdb=" CB  VAL C 119 "
            pdb=" CA  VAL C 119 "
            pdb=" CG1 VAL C 119 "
            pdb=" CG2 VAL C 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  VAL E  82 "
            pdb=" CA  VAL E  82 "
            pdb=" CG1 VAL E  82 "
            pdb=" CG2 VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CA  LYS H  31 "
            pdb=" N   LYS H  31 "
            pdb=" C   LYS H  31 "
            pdb=" CB  LYS H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 1633 not shown)

  Planarity restraints: 1016
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J   5 "   -0.005 2.00e-02 2.50e+03   1.18e-02 3.11e+00
        pdb=" N1   DC J   5 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DC J   5 "   -0.028 2.00e-02 2.50e+03
        pdb=" O2   DC J   5 "    0.019 2.00e-02 2.50e+03
        pdb=" N3   DC J   5 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC J   5 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J   5 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J   5 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "   -0.021 2.00e-02 2.50e+03   9.48e-03 2.47e+00
        pdb=" N9   DA I  17 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  -4 "    0.017 2.00e-02 2.50e+03   9.91e-03 2.21e+00
        pdb=" N1   DC I  -4 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2   DC I  -4 "    0.012 2.00e-02 2.50e+03
        pdb=" O2   DC I  -4 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC I  -4 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DC I  -4 "    0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  -4 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DC I  -4 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC I  -4 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1013 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 28
        2.52 -     3.12: 6589
        3.12 -     3.71: 17762
        3.71 -     4.31: 22316
        4.31 -     4.90: 31856
  Nonbonded interactions: 78551
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 112 "
            pdb=" OD1 ASP A 125 "
     model   vdw
     1.931 3.460
  nonbonded pdb=" CG2 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.121 3.460
  nonbonded pdb=" OG1 THR F  30 "
            pdb=" OP1  DT I  18 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" NH2 ARG H  36 "
            pdb=" OP2  DG J -44 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" OD2 ASP C 108 "
            pdb=" NH1 ARG C 133 "
     model   vdw
     2.250 3.120
  ... (remaining 78546 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 65 through 134)
  selection = (chain 'C' and resid 65 through 134)
  selection = (chain 'E' and resid 65 through 134)
  selection = (chain 'G' and resid 65 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and resid 26 through 90)
  selection = (chain 'F' and resid 26 through 90)
  selection = (chain 'H' and resid 26 through 90)
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.880
  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:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.980
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
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   0.044   9844  Z= 0.258
  Angle     :  0.653   6.932  14265  Z= 0.404
  Chirality :  0.036   0.207   1636
  Planarity :  0.003   0.024   1016
  Dihedral  : 29.322 178.070   4275
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.35), residues: 558
  helix:  1.74 (0.25), residues: 429
  sheet:  None (None), residues: 0
  loop : -1.55 (0.46), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.022   0.001   PHE C  78 
 TYR   0.017   0.001   TYR E 110 
 ARG   0.003   0.000   ARG H  67 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7457 (t80) cc_final: 0.7201 (t80)
REVERT: A   99 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6588 (mp0)
REVERT: A  110 TYR cc_start: 0.8249 (t80) cc_final: 0.7890 (t80)
REVERT: B   44 LYS cc_start: 0.8753 (mmpt) cc_final: 0.8545 (mmmt)
REVERT: B   50 ILE cc_start: 0.8803 (tt) cc_final: 0.8487 (mt)
REVERT: C   96 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6726 (tm-30)
REVERT: F   50 ILE cc_start: 0.8573 (tp) cc_final: 0.8358 (tp)
REVERT: H   49 LEU cc_start: 0.8649 (tp) cc_final: 0.8146 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2977
  time to fit residues: 64.5132
Evaluate side-chains
  120 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
C 104 HIS
** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  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 = 0.3416 r_free = 0.3416 target = 0.046140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.034920 restraints weight = 82251.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.035883 restraints weight = 45443.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.036471 restraints weight = 31372.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9844  Z= 0.223
  Angle     :  0.650  11.869  14265  Z= 0.383
  Chirality :  0.036   0.232   1636
  Planarity :  0.004   0.031   1016
  Dihedral  : 32.414 179.856   3157
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.34), residues: 558
  helix:  1.90 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  86 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.026   0.002   PHE C  78 
 TYR   0.020   0.002   TYR D  88 
 ARG   0.004   0.001   ARG E  72 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7128 (mp0)
REVERT: A  107 GLU cc_start: 0.9096 (pt0) cc_final: 0.8709 (pt0)
REVERT: A  110 TYR cc_start: 0.9084 (t80) cc_final: 0.8843 (t80)
REVERT: B   44 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8672 (mmmt)
REVERT: B   50 ILE cc_start: 0.9396 (tt) cc_final: 0.9182 (mm)
REVERT: B   59 LYS cc_start: 0.9658 (tmtt) cc_final: 0.9220 (tmtt)
REVERT: B   85 ASP cc_start: 0.7385 (m-30) cc_final: 0.6883 (m-30)
REVERT: C   73 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8663 (tm-30)
REVERT: C  124 LYS cc_start: 0.9343 (pttp) cc_final: 0.8949 (pttp)
REVERT: C  130 ARG cc_start: 0.9214 (ttp80) cc_final: 0.8650 (tpt90)
REVERT: D   92 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8466 (tpt90)
REVERT: E   73 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: E   87 GLN cc_start: 0.9413 (tt0) cc_final: 0.8720 (mt0)
REVERT: E   89 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8354 (tp40)
REVERT: E   99 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: F   50 ILE cc_start: 0.9418 (tp) cc_final: 0.9198 (tp)
REVERT: F   63 GLU cc_start: 0.8884 (tp30) cc_final: 0.8655 (tp30)
REVERT: G   96 GLU cc_start: 0.9125 (pp20) cc_final: 0.8896 (pp20)
REVERT: G  101 PHE cc_start: 0.9385 (t80) cc_final: 0.8902 (t80)
REVERT: G  107 GLU cc_start: 0.9248 (pt0) cc_final: 0.8915 (pp20)
REVERT: G  110 TYR cc_start: 0.9351 (t80) cc_final: 0.9009 (t80)
REVERT: H   53 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9221 (tt0)
REVERT: H   68 ASP cc_start: 0.9121 (t70) cc_final: 0.8820 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.3060
  time to fit residues: 63.9275
Evaluate side-chains
  126 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    3.5986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.042212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.031202 restraints weight = 86253.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.032045 restraints weight = 47888.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.032616 restraints weight = 33290.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   9844  Z= 0.363
  Angle     :  0.723   8.511  14265  Z= 0.421
  Chirality :  0.039   0.249   1636
  Planarity :  0.005   0.032   1016
  Dihedral  : 33.053 178.662   3157
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 20.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  7.14 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.33), residues: 558
  helix:  1.71 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.83 (0.44), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  86 
 HIS   0.007   0.002   HIS E 115 
 PHE   0.026   0.002   PHE C  78 
 TYR   0.012   0.002   TYR B  51 
 ARG   0.006   0.001   ARG H  67 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8506 (t80) cc_final: 0.8215 (t80)
REVERT: A   99 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7149 (mp0)
REVERT: A  110 TYR cc_start: 0.9071 (t80) cc_final: 0.8771 (t80)
REVERT: B   44 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8674 (mmmt)
REVERT: B   84 MET cc_start: 0.7087 (mmp) cc_final: 0.6443 (mmp)
REVERT: B   85 ASP cc_start: 0.7545 (m-30) cc_final: 0.6906 (m-30)
REVERT: C   73 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: C   96 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7336 (tm-30)
REVERT: C  104 HIS cc_start: 0.8509 (m-70) cc_final: 0.8100 (m-70)
REVERT: C  107 GLU cc_start: 0.8988 (pt0) cc_final: 0.8589 (pp20)
REVERT: C  130 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8650 (tpt90)
REVERT: C  131 ARG cc_start: 0.9060 (ptp-110) cc_final: 0.8824 (ttp-110)
REVERT: D   44 LYS cc_start: 0.9502 (mmtm) cc_final: 0.9183 (mmtt)
REVERT: D   63 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: D   64 ASN cc_start: 0.9285 (m-40) cc_final: 0.8959 (m-40)
REVERT: D   74 GLU cc_start: 0.9198 (tp30) cc_final: 0.8991 (tp30)
REVERT: E   87 GLN cc_start: 0.9283 (tt0) cc_final: 0.8680 (mt0)
REVERT: E   89 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8152 (tp-100)
REVERT: E   96 GLU cc_start: 0.8838 (tp30) cc_final: 0.8612 (tp30)
REVERT: F   50 ILE cc_start: 0.9409 (tp) cc_final: 0.9129 (tp)
REVERT: G  101 PHE cc_start: 0.9408 (t80) cc_final: 0.8946 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2657
  time to fit residues: 50.4861
Evaluate side-chains
  119 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.041987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.031101 restraints weight = 86819.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.031966 restraints weight = 47714.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.032539 restraints weight = 32974.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9844  Z= 0.317
  Angle     :  0.693  10.355  14265  Z= 0.407
  Chirality :  0.038   0.253   1636
  Planarity :  0.004   0.032   1016
  Dihedral  : 33.188 179.150   3157
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.25 %
    Favored  : 94.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.34), residues: 558
  helix:  1.76 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.85 (0.44), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.022   0.002   PHE C  78 
 TYR   0.024   0.002   TYR E 110 
 ARG   0.011   0.001   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8601 (t80) cc_final: 0.8270 (t80)
REVERT: A   99 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7230 (mp0)
REVERT: A  107 GLU cc_start: 0.9108 (pt0) cc_final: 0.8696 (pt0)
REVERT: B   44 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8681 (mmmt)
REVERT: B   59 LYS cc_start: 0.9740 (tmtt) cc_final: 0.9465 (tptt)
REVERT: B   84 MET cc_start: 0.7210 (mmp) cc_final: 0.6333 (mmp)
REVERT: B   85 ASP cc_start: 0.7633 (m-30) cc_final: 0.6823 (m-30)
REVERT: C   73 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8664 (tm-30)
REVERT: C  107 GLU cc_start: 0.9004 (pt0) cc_final: 0.8792 (pt0)
REVERT: C  130 ARG cc_start: 0.9202 (ttp80) cc_final: 0.8670 (tpt90)
REVERT: D   44 LYS cc_start: 0.9522 (mmtm) cc_final: 0.9249 (mmtt)
REVERT: D   63 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: D   67 ARG cc_start: 0.8976 (ttp-170) cc_final: 0.8675 (ttp80)
REVERT: D   68 ASP cc_start: 0.8806 (m-30) cc_final: 0.8558 (m-30)
REVERT: D   92 ARG cc_start: 0.8799 (tpt90) cc_final: 0.8590 (tpt90)
REVERT: E   87 GLN cc_start: 0.9328 (tt0) cc_final: 0.8673 (mt0)
REVERT: E   89 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8048 (tp-100)
REVERT: E   96 GLU cc_start: 0.8998 (tp30) cc_final: 0.8590 (tp30)
REVERT: E  130 ARG cc_start: 0.8985 (tpt-90) cc_final: 0.8589 (tpt90)
REVERT: F   49 LEU cc_start: 0.9547 (mp) cc_final: 0.8914 (mp)
REVERT: F   50 ILE cc_start: 0.9425 (tp) cc_final: 0.8979 (tp)
REVERT: G  101 PHE cc_start: 0.9438 (t80) cc_final: 0.9030 (t80)
REVERT: G  110 TYR cc_start: 0.9360 (t80) cc_final: 0.8861 (t80)
REVERT: H   49 LEU cc_start: 0.9163 (tp) cc_final: 0.8685 (tp)
REVERT: H   67 ARG cc_start: 0.9587 (tpp80) cc_final: 0.9193 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.3013
  time to fit residues: 58.5276
Evaluate side-chains
  116 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    3.5990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.041000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.030278 restraints weight = 87499.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.031129 restraints weight = 48139.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.031693 restraints weight = 33300.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9844  Z= 0.349
  Angle     :  0.713  10.546  14265  Z= 0.415
  Chirality :  0.040   0.291   1636
  Planarity :  0.004   0.030   1016
  Dihedral  : 33.434 178.822   3157
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.34), residues: 558
  helix:  1.66 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.97 (0.43), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  86 
 HIS   0.010   0.002   HIS E 115 
 PHE   0.023   0.002   PHE C  78 
 TYR   0.022   0.002   TYR E 110 
 ARG   0.015   0.001   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8689 (t80) cc_final: 0.8282 (t80)
REVERT: A   99 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7426 (mt-10)
REVERT: A  107 GLU cc_start: 0.9116 (pt0) cc_final: 0.8731 (pt0)
REVERT: A  110 TYR cc_start: 0.9092 (t80) cc_final: 0.8772 (t80)
REVERT: B   44 LYS cc_start: 0.9136 (mmpt) cc_final: 0.8806 (mmmt)
REVERT: B   84 MET cc_start: 0.7582 (mmp) cc_final: 0.7262 (mmp)
REVERT: B   85 ASP cc_start: 0.7526 (m-30) cc_final: 0.6802 (m-30)
REVERT: C   73 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: C   96 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: C  107 GLU cc_start: 0.9014 (pt0) cc_final: 0.8774 (pt0)
REVERT: C  130 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8654 (tpt90)
REVERT: D   63 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: D   67 ARG cc_start: 0.8945 (ttp-170) cc_final: 0.8644 (ttp80)
REVERT: D   68 ASP cc_start: 0.8818 (m-30) cc_final: 0.8568 (m-30)
REVERT: D   92 ARG cc_start: 0.8707 (tpt90) cc_final: 0.8499 (tpt90)
REVERT: E   87 GLN cc_start: 0.9269 (tt0) cc_final: 0.8655 (mt0)
REVERT: E   89 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8106 (tp-100)
REVERT: E   96 GLU cc_start: 0.8988 (tp30) cc_final: 0.8598 (tp30)
REVERT: E  130 ARG cc_start: 0.8942 (tpt-90) cc_final: 0.8546 (tpt90)
REVERT: F   49 LEU cc_start: 0.9512 (mp) cc_final: 0.9088 (tp)
REVERT: F   50 ILE cc_start: 0.9434 (tp) cc_final: 0.9108 (tp)
REVERT: G  101 PHE cc_start: 0.9420 (t80) cc_final: 0.9058 (t80)
REVERT: G  110 TYR cc_start: 0.9369 (t80) cc_final: 0.9065 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2571
  time to fit residues: 46.3223
Evaluate side-chains
  114 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0570
   chunk 65 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.3502

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.043120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.032544 restraints weight = 82984.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033467 restraints weight = 45423.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.034050 restraints weight = 31099.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9844  Z= 0.205
  Angle     :  0.664  12.109  14265  Z= 0.387
  Chirality :  0.037   0.176   1636
  Planarity :  0.004   0.033   1016
  Dihedral  : 33.192 179.797   3157
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.34), residues: 558
  helix:  1.84 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.73 (0.43), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.017   0.002   PHE C  78 
 TYR   0.023   0.002   TYR E 110 
 ARG   0.011   0.000   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8597 (t80) cc_final: 0.8229 (t80)
REVERT: A   99 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7258 (mp0)
REVERT: A  107 GLU cc_start: 0.9134 (pt0) cc_final: 0.8704 (pt0)
REVERT: B   44 LYS cc_start: 0.9168 (mmpt) cc_final: 0.8648 (mmmt)
REVERT: B   59 LYS cc_start: 0.9724 (tmtt) cc_final: 0.9356 (tmtt)
REVERT: B   84 MET cc_start: 0.7520 (mmp) cc_final: 0.7119 (mmp)
REVERT: B   85 ASP cc_start: 0.7576 (m-30) cc_final: 0.6687 (m-30)
REVERT: C   73 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8675 (tm-30)
REVERT: C  107 GLU cc_start: 0.8996 (pt0) cc_final: 0.8737 (pt0)
REVERT: C  130 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8629 (tpt90)
REVERT: D   63 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: D   67 ARG cc_start: 0.8936 (ttp-170) cc_final: 0.8631 (ttp80)
REVERT: D   68 ASP cc_start: 0.8737 (m-30) cc_final: 0.8441 (m-30)
REVERT: E   73 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: E   87 GLN cc_start: 0.9298 (tt0) cc_final: 0.8890 (mt0)
REVERT: E   89 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8012 (tp-100)
REVERT: E   96 GLU cc_start: 0.8901 (tp30) cc_final: 0.8458 (tp30)
REVERT: F   49 LEU cc_start: 0.9388 (mp) cc_final: 0.9102 (tt)
REVERT: F   50 ILE cc_start: 0.9332 (tp) cc_final: 0.8986 (tp)
REVERT: F   82 THR cc_start: 0.9197 (m) cc_final: 0.8841 (p)
REVERT: F   92 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.8090 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9400 (t80) cc_final: 0.9014 (t80)
REVERT: G  107 GLU cc_start: 0.9160 (pt0) cc_final: 0.8744 (pp20)
REVERT: G  110 TYR cc_start: 0.9348 (t80) cc_final: 0.9063 (t80)
REVERT: H   49 LEU cc_start: 0.9175 (tp) cc_final: 0.8721 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2796
  time to fit residues: 56.0471
Evaluate side-chains
  120 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    0.4980
   chunk 50 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   overall best weight:    3.0986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.041306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.030807 restraints weight = 86985.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.031707 restraints weight = 47268.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.032298 restraints weight = 32258.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9844  Z= 0.324
  Angle     :  0.718   8.999  14265  Z= 0.416
  Chirality :  0.039   0.225   1636
  Planarity :  0.004   0.030   1016
  Dihedral  : 33.448 178.330   3157
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.33), residues: 558
  helix:  1.69 (0.24), residues: 423
  sheet:  None (None), residues: 0
  loop : -1.84 (0.43), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  86 
 HIS   0.006   0.001   HIS E 115 
 PHE   0.023   0.002   PHE D  61 
 TYR   0.026   0.002   TYR E 110 
 ARG   0.011   0.001   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8644 (t80) cc_final: 0.8306 (t80)
REVERT: A   99 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7412 (mt-10)
REVERT: A  107 GLU cc_start: 0.9134 (pt0) cc_final: 0.8720 (pt0)
REVERT: A  110 TYR cc_start: 0.9121 (t80) cc_final: 0.8818 (t80)
REVERT: B   44 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8806 (mmmt)
REVERT: B   59 LYS cc_start: 0.9721 (tmtt) cc_final: 0.9304 (tmtt)
REVERT: B   84 MET cc_start: 0.7666 (mmp) cc_final: 0.7311 (mmp)
REVERT: B   85 ASP cc_start: 0.7443 (m-30) cc_final: 0.6612 (m-30)
REVERT: C   73 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8648 (tm-30)
REVERT: C  107 GLU cc_start: 0.8980 (pt0) cc_final: 0.8724 (pt0)
REVERT: C  130 ARG cc_start: 0.9207 (ttp80) cc_final: 0.8607 (tpt90)
REVERT: D   63 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: D   67 ARG cc_start: 0.8984 (ttp-170) cc_final: 0.8668 (ttp80)
REVERT: D   68 ASP cc_start: 0.8796 (m-30) cc_final: 0.8572 (m-30)
REVERT: D   92 ARG cc_start: 0.8676 (tpt90) cc_final: 0.8418 (tpt90)
REVERT: E   87 GLN cc_start: 0.9306 (tt0) cc_final: 0.8801 (mt0)
REVERT: E   89 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8124 (tp-100)
REVERT: E   96 GLU cc_start: 0.8972 (tp30) cc_final: 0.8546 (tp30)
REVERT: F   50 ILE cc_start: 0.9360 (tp) cc_final: 0.9035 (tp)
REVERT: F   92 ARG cc_start: 0.8505 (tpt-90) cc_final: 0.7998 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9387 (t80) cc_final: 0.9112 (t80)
REVERT: G  107 GLU cc_start: 0.9242 (pt0) cc_final: 0.8860 (pp20)
REVERT: G  110 TYR cc_start: 0.9398 (t80) cc_final: 0.8990 (t80)
REVERT: H   44 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8632 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2623
  time to fit residues: 47.4933
Evaluate side-chains
  108 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.043365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.032733 restraints weight = 85114.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.033646 restraints weight = 46743.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.034223 restraints weight = 32043.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9844  Z= 0.203
  Angle     :  0.687  11.029  14265  Z= 0.393
  Chirality :  0.037   0.188   1636
  Planarity :  0.004   0.033   1016
  Dihedral  : 33.192 179.355   3157
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.34), residues: 558
  helix:  1.80 (0.24), residues: 423
  sheet:  None (None), residues: 0
  loop : -1.64 (0.43), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.018   0.002   PHE D  61 
 TYR   0.028   0.002   TYR E 110 
 ARG   0.013   0.001   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8616 (t80) cc_final: 0.8244 (t80)
REVERT: A   99 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7296 (mp0)
REVERT: A  107 GLU cc_start: 0.9146 (pt0) cc_final: 0.8696 (pt0)
REVERT: A  110 TYR cc_start: 0.9098 (t80) cc_final: 0.8877 (t80)
REVERT: B   44 LYS cc_start: 0.9100 (mmpt) cc_final: 0.8755 (mmmt)
REVERT: B   59 LYS cc_start: 0.9731 (tmtt) cc_final: 0.9292 (tmtt)
REVERT: B   84 MET cc_start: 0.7711 (mmp) cc_final: 0.7311 (mmp)
REVERT: B   85 ASP cc_start: 0.7504 (m-30) cc_final: 0.6613 (m-30)
REVERT: C   73 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: C  107 GLU cc_start: 0.8965 (pt0) cc_final: 0.8713 (pt0)
REVERT: C  130 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8636 (tpt90)
REVERT: D   63 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: D   67 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.8566 (ttp80)
REVERT: D   68 ASP cc_start: 0.8622 (m-30) cc_final: 0.8388 (m-30)
REVERT: D   92 ARG cc_start: 0.8648 (tpt90) cc_final: 0.8387 (tpt90)
REVERT: E   73 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8515 (tm-30)
REVERT: E   87 GLN cc_start: 0.9230 (tt0) cc_final: 0.8825 (mt0)
REVERT: E   89 GLN cc_start: 0.8390 (tp-100) cc_final: 0.7980 (tp-100)
REVERT: F   50 ILE cc_start: 0.9322 (tp) cc_final: 0.9005 (tp)
REVERT: F   92 ARG cc_start: 0.8456 (tpt-90) cc_final: 0.7905 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9345 (t80) cc_final: 0.8986 (t80)
REVERT: G  107 GLU cc_start: 0.9221 (pt0) cc_final: 0.8845 (pp20)
REVERT: G  108 ASP cc_start: 0.8833 (m-30) cc_final: 0.7653 (m-30)
REVERT: G  110 TYR cc_start: 0.9325 (t80) cc_final: 0.8968 (t80)
REVERT: H   39 ARG cc_start: 0.8983 (tpt90) cc_final: 0.8595 (tpt90)
REVERT: H   44 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8637 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.3021
  time to fit residues: 59.5095
Evaluate side-chains
  120 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   overall best weight:    3.3990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.041133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.030632 restraints weight = 86204.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.031482 restraints weight = 47995.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.032069 restraints weight = 33242.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9844  Z= 0.342
  Angle     :  0.742   9.597  14265  Z= 0.425
  Chirality :  0.040   0.191   1636
  Planarity :  0.004   0.030   1016
  Dihedral  : 33.541 177.767   3157
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.33), residues: 558
  helix:  1.58 (0.24), residues: 421
  sheet:  None (None), residues: 0
  loop : -1.86 (0.43), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  86 
 HIS   0.006   0.001   HIS E 115 
 PHE   0.024   0.002   PHE D  61 
 TYR   0.023   0.002   TYR E 110 
 ARG   0.006   0.001   ARG F  67 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8671 (t80) cc_final: 0.8270 (t80)
REVERT: A   72 ARG cc_start: 0.8958 (mmp80) cc_final: 0.8738 (mmp80)
REVERT: A   85 ASN cc_start: 0.9413 (m110) cc_final: 0.9211 (m110)
REVERT: A   99 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: A  107 GLU cc_start: 0.9135 (pt0) cc_final: 0.8703 (pt0)
REVERT: A  110 TYR cc_start: 0.9121 (t80) cc_final: 0.8816 (t80)
REVERT: B   44 LYS cc_start: 0.9153 (mmpt) cc_final: 0.8832 (mmmt)
REVERT: B   59 LYS cc_start: 0.9686 (tmtt) cc_final: 0.9390 (tmtt)
REVERT: B   84 MET cc_start: 0.7922 (mmp) cc_final: 0.7574 (mmp)
REVERT: B   85 ASP cc_start: 0.7484 (m-30) cc_final: 0.6648 (m-30)
REVERT: C   73 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: C  107 GLU cc_start: 0.8986 (pt0) cc_final: 0.8749 (pt0)
REVERT: C  130 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8654 (tpt90)
REVERT: D   63 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: D   67 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8636 (ttp80)
REVERT: D   68 ASP cc_start: 0.8751 (m-30) cc_final: 0.8542 (m-30)
REVERT: E   87 GLN cc_start: 0.9247 (tt0) cc_final: 0.8754 (mt0)
REVERT: E   89 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8160 (tp-100)
REVERT: F   50 ILE cc_start: 0.9371 (tp) cc_final: 0.9079 (tp)
REVERT: F   92 ARG cc_start: 0.8482 (tpt-90) cc_final: 0.8034 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9350 (t80) cc_final: 0.9135 (t80)
REVERT: G  107 GLU cc_start: 0.9240 (pt0) cc_final: 0.8907 (pp20)
REVERT: G  108 ASP cc_start: 0.8936 (m-30) cc_final: 0.7755 (m-30)
REVERT: G  110 TYR cc_start: 0.9342 (t80) cc_final: 0.9021 (t80)
REVERT: H   39 ARG cc_start: 0.9063 (tpt90) cc_final: 0.8730 (tpt90)
REVERT: H   44 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8724 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.3037
  time to fit residues: 51.3742
Evaluate side-chains
  109 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 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 = 0.3361 r_free = 0.3361 target = 0.043426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.032892 restraints weight = 84033.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.033820 restraints weight = 46216.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.034444 restraints weight = 31466.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9844  Z= 0.202
  Angle     :  0.696   9.989  14265  Z= 0.397
  Chirality :  0.037   0.177   1636
  Planarity :  0.004   0.043   1016
  Dihedral  : 33.200 179.771   3157
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.34), residues: 558
  helix:  1.73 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.81 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.019   0.001   PHE D  61 
 TYR   0.023   0.002   TYR E 110 
 ARG   0.023   0.001   ARG A  69 

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8627 (t80) cc_final: 0.8198 (t80)
REVERT: A   99 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7291 (mp0)
REVERT: A  107 GLU cc_start: 0.9152 (pt0) cc_final: 0.8694 (pt0)
REVERT: A  110 TYR cc_start: 0.9060 (t80) cc_final: 0.8822 (t80)
REVERT: B   44 LYS cc_start: 0.9100 (mmpt) cc_final: 0.8745 (mmmt)
REVERT: B   59 LYS cc_start: 0.9683 (tmtt) cc_final: 0.9273 (tmtt)
REVERT: B   84 MET cc_start: 0.7795 (mmp) cc_final: 0.7370 (mmp)
REVERT: B   85 ASP cc_start: 0.7440 (m-30) cc_final: 0.6485 (m-30)
REVERT: C   73 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: C  107 GLU cc_start: 0.8953 (pt0) cc_final: 0.8701 (pt0)
REVERT: C  130 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8649 (tpt90)
REVERT: D   63 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: D   67 ARG cc_start: 0.8887 (ttp-170) cc_final: 0.8548 (ttp80)
REVERT: D   68 ASP cc_start: 0.8583 (m-30) cc_final: 0.8332 (m-30)
REVERT: D   74 GLU cc_start: 0.9027 (tp30) cc_final: 0.8826 (tp30)
REVERT: E   87 GLN cc_start: 0.9196 (tt0) cc_final: 0.8818 (mt0)
REVERT: E   89 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7916 (tp-100)
REVERT: E   96 GLU cc_start: 0.8881 (tt0) cc_final: 0.8645 (tt0)
REVERT: F   50 ILE cc_start: 0.9294 (tp) cc_final: 0.8983 (tp)
REVERT: F   92 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.7855 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9323 (t80) cc_final: 0.8994 (t80)
REVERT: G  107 GLU cc_start: 0.9229 (pt0) cc_final: 0.8869 (pp20)
REVERT: G  108 ASP cc_start: 0.8813 (m-30) cc_final: 0.7696 (m-30)
REVERT: H   39 ARG cc_start: 0.8983 (tpt90) cc_final: 0.8579 (tpt90)
REVERT: H   44 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8711 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2821
  time to fit residues: 55.1913
Evaluate side-chains
  119 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 15 optimal weight:    0.3980
   chunk 63 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.4184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.042056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.031594 restraints weight = 85281.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.032476 restraints weight = 47549.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.033056 restraints weight = 32792.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9844  Z= 0.271
  Angle     :  0.705   9.108  14265  Z= 0.406
  Chirality :  0.038   0.187   1636
  Planarity :  0.004   0.054   1016
  Dihedral  : 33.365 178.883   3157
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.34), residues: 558
  helix:  1.65 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.91 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  86 
 HIS   0.007   0.001   HIS E 115 
 PHE   0.023   0.002   PHE D  61 
 TYR   0.026   0.002   TYR E 110 
 ARG   0.014   0.001   ARG A  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2662.20 seconds
wall clock time: 48 minutes 56.65 seconds (2936.65 seconds total)