Starting phenix.real_space_refine
on Sun Apr  5 17:04:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10yd_75525/04_2026/10yd_75525.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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     294      5.49       5
     S      10      5.16       5
     C    6601      2.51       5
     N    2240      2.21       5
     O    2814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11959
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 793
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 310
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "K"
      Number of atoms: 2722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 2722
          Classifications: {'DNA': 132}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 131}
  Time building chain proxies: 2.14, per 1000 atoms: 0.18
  Number of scatterers: 11959
  At special positions: 0
  Unit cell: (74.328, 123.88, 118.664, 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      10     16.00
     P     294     15.00
     O    2814      8.00
     N    2240      7.00
     C    6601      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 362.7 milliseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      74.1% alpha, 2.7% beta
      147 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 1.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 3.544A  pdb=" N   TYR A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.982A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.544A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.365A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.511A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.509A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 57
      removed outlier: 4.173A  pdb=" N   VAL E  46 " --> pdb=" O   ARG E  42 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ALA E  47 " --> pdb=" O   PRO E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.082A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.658A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.547A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.318A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.151A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.599A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.340A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.925A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.293A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    399 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      752 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2117
        1.33 -     1.45: 4288
        1.45 -     1.57: 5760
        1.57 -     1.69: 586
        1.69 -     1.81: 20
  Bond restraints: 12771
  Sorted by residual:
  bond pdb=" N   LYS C  36 "
       pdb=" CA  LYS C  36 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.26e-02 6.30e+03 7.50e+00
  bond pdb=" N   GLU H  35 "
       pdb=" CA  GLU H  35 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.22e-02 6.72e+03 6.43e+00
  bond pdb=" N   VAL G 107 "
       pdb=" CA  VAL G 107 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.028 1.11e-02 8.12e+03 6.26e+00
  bond pdb=" N   LYS H  34 "
       pdb=" CA  LYS H  34 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 5.91e+00
  bond pdb=" N   ASN H  63 "
       pdb=" CA  ASN H  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.90e+00
  ... (remaining 12766 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 18009
        1.68 -     3.36: 461
        3.36 -     5.04: 22
        5.04 -     6.72: 9
        6.72 -     8.39: 8
  Bond angle restraints: 18509
  Sorted by residual:
  angle pdb=" N   GLN G  24 "
        pdb=" CA  GLN G  24 "
        pdb=" C   GLN G  24 "
      ideal   model   delta    sigma   weight residual
     113.88  108.19    5.69 1.23e+00 6.61e-01 2.14e+01
  angle pdb=" CB  GLU C  91 "
        pdb=" CG  GLU C  91 "
        pdb=" CD  GLU C  91 "
      ideal   model   delta    sigma   weight residual
     112.60  119.45   -6.85 1.70e+00 3.46e-01 1.63e+01
  angle pdb=" CA  GLU C  91 "
        pdb=" CB  GLU C  91 "
        pdb=" CG  GLU C  91 "
      ideal   model   delta    sigma   weight residual
     114.10  122.10   -8.00 2.00e+00 2.50e-01 1.60e+01
  angle pdb=" CG  ARG G  71 "
        pdb=" CD  ARG G  71 "
        pdb=" NE  ARG G  71 "
      ideal   model   delta    sigma   weight residual
     112.00  119.50   -7.50 2.20e+00 2.07e-01 1.16e+01
  angle pdb=" CA  ASP A  81 "
        pdb=" CB  ASP A  81 "
        pdb=" CG  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     112.60  115.84   -3.24 1.00e+00 1.00e+00 1.05e+01
  ... (remaining 18504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.57: 5033
       28.57 -    57.14: 1729
       57.14 -    85.71: 151
       85.71 -   114.28: 1
      114.28 -   142.86: 2
  Dihedral angle restraints: 6916
    sinusoidal: 4750
      harmonic: 2166
  Sorted by residual:
  dihedral pdb=" CD  ARG H  33 "
           pdb=" NE  ARG H  33 "
           pdb=" CZ  ARG H  33 "
           pdb=" NH1 ARG H  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -45.11   45.11     1      1.00e+01 1.00e-02 2.83e+01
  dihedral pdb=" CD  ARG A  40 "
           pdb=" NE  ARG A  40 "
           pdb=" CZ  ARG A  40 "
           pdb=" NH1 ARG A  40 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -41.25   41.25     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CA  LEU A  48 "
           pdb=" C   LEU A  48 "
           pdb=" N   ARG A  49 "
           pdb=" CA  ARG A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 6913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1662
       0.041 -    0.082: 368
       0.082 -    0.123: 66
       0.123 -    0.164: 10
       0.164 -    0.205: 2
  Chirality restraints: 2108
  Sorted by residual:
  chirality pdb=" CA  VAL G 107 "
            pdb=" N   VAL G 107 "
            pdb=" C   VAL G 107 "
            pdb=" CB  VAL G 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" CA  PRO E  43 "
            pdb=" N   PRO E  43 "
            pdb=" C   PRO E  43 "
            pdb=" CB  PRO E  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.08e-01
  ... (remaining 2105 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  33 "    0.775 9.50e-02 1.11e+02   3.47e-01 7.34e+01
        pdb=" NE  ARG H  33 "   -0.046 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  33 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  33 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  33 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  40 "    0.732 9.50e-02 1.11e+02   3.28e-01 6.56e+01
        pdb=" NE  ARG A  40 "   -0.043 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  40 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  40 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  40 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  58 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.90e+00
        pdb=" C   THR A  58 "    0.038 2.00e-02 2.50e+03
        pdb=" O   THR A  58 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLU A  59 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1319 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.01: 5639
        3.01 -     3.48: 11328
        3.48 -     3.95: 24553
        3.95 -     4.43: 27404
        4.43 -     4.90: 35526
  Nonbonded interactions: 104450
  Sorted by model distance:
  nonbonded pdb=" O5'  DA I 124 "
            pdb=" O4'  DA I 124 "
     model   vdw
     2.533 2.432
  nonbonded pdb=" N   ILE C  79 "
            pdb=" O   ILE C  79 "
     model   vdw
     2.590 2.496
  nonbonded pdb=" N   ILE G  79 "
            pdb=" O   ILE G  79 "
     model   vdw
     2.592 2.496
  nonbonded pdb=" N1   DG K 120 "
            pdb=" C4   DG K 120 "
     model   vdw
     2.593 2.672
  nonbonded pdb=" N1   DG I  40 "
            pdb=" C4   DG I  40 "
     model   vdw
     2.594 2.672
  ... (remaining 104445 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 'E' and resid 38 through 133)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 15 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 33 through 124)
  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 individual isotropic
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:             6.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.810
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:6.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
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   0.051  12771  Z= 0.206
  Angle     :  0.620   8.394  18509  Z= 0.373
  Chirality :  0.036   0.205   2108
  Planarity :  0.014   0.347   1322
  Dihedral  : 28.326 142.855   5520
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 20.10 %
    Favored  : 79.58 %
  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 are not related in a simple way.
  whole:  1.38 (0.30), residues: 732
  helix:  1.48 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.60 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  71 
 TYR   0.013   0.001   TYR D  40 
 PHE   0.008   0.002   PHE C  25 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (12771)
  covalent geometry    : angle       0.62040 (18509)
  hydrogen bonds       : bond        0.11085 (  775)
  hydrogen bonds       : angle       4.15265 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7924 (mtp85)
REVERT: C   90 ASP cc_start: 0.8599 (t0) cc_final: 0.8017 (t70)
REVERT: D   42 TYR cc_start: 0.8226 (t80) cc_final: 0.7966 (m-80)
REVERT: G   64 GLU cc_start: 0.8632 (tt0) cc_final: 0.8345 (tp30)
REVERT: G   71 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8348 (ttp80)
REVERT: G   73 ASN cc_start: 0.8789 (t0) cc_final: 0.8048 (t0)
REVERT: G   91 GLU cc_start: 0.8975 (tp30) cc_final: 0.8699 (tp30)
REVERT: H   63 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8467 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.9004
  time to fit residues: 152.5513
Evaluate side-chains
  158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  25 ASN
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.099913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.067262 restraints weight = 21528.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.50
r_work: 0.2756 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.0432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12771  Z= 0.171
  Angle     :  0.550   5.722  18509  Z= 0.334
  Chirality :  0.033   0.131   2108
  Planarity :  0.004   0.075   1322
  Dihedral  : 30.495 142.467   4045
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.01 %
    Favored  : 80.23 %
  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 are not related in a simple way.
  whole:  2.21 (0.30), residues: 732
  helix:  2.07 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.42 (0.43), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  40 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12771)
  covalent geometry    : angle       0.54962 (18509)
  hydrogen bonds       : bond        0.04407 (  775)
  hydrogen bonds       : angle       3.18468 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7870 (mtp85)
REVERT: G   64 GLU cc_start: 0.8629 (tt0) cc_final: 0.8315 (tp30)
REVERT: G   73 ASN cc_start: 0.8739 (t0) cc_final: 0.8000 (t0)
REVERT: G   91 GLU cc_start: 0.8736 (tp30) cc_final: 0.8520 (tp30)
REVERT: H   63 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8480 (m-40)
  outliers start: 11
  outliers final: 3
  residues processed: 159
  average time/residue: 0.8753
  time to fit residues: 146.6695
Evaluate side-chains
  158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0870
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0980
   overall best weight:    1.6362

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.099114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066346 restraints weight = 21793.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.52
r_work: 0.2736 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2596 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.0604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  12771  Z= 0.218
  Angle     :  0.552   5.321  18509  Z= 0.334
  Chirality :  0.034   0.140   2108
  Planarity :  0.004   0.040   1322
  Dihedral  : 30.471 142.457   4045
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.04 %
    Favored  : 80.06 %
  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 are not related in a simple way.
  whole:  2.43 (0.31), residues: 732
  helix:  2.27 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.47 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  71 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (12771)
  covalent geometry    : angle       0.55171 (18509)
  hydrogen bonds       : bond        0.04211 (  775)
  hydrogen bonds       : angle       2.97646 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7881 (mtp85)
REVERT: B   77 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8751 (mtpt)
REVERT: C   64 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8304 (tt0)
REVERT: G   73 ASN cc_start: 0.8715 (t0) cc_final: 0.7970 (t0)
REVERT: G   91 GLU cc_start: 0.8686 (tp30) cc_final: 0.8473 (tp30)
REVERT: H   63 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8605 (m-40)
  outliers start: 18
  outliers final: 7
  residues processed: 162
  average time/residue: 0.8703
  time to fit residues: 148.4683
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.098533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.065649 restraints weight = 21601.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.52
r_work: 0.2719 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12771  Z= 0.232
  Angle     :  0.555   5.447  18509  Z= 0.337
  Chirality :  0.035   0.143   2108
  Planarity :  0.004   0.055   1322
  Dihedral  : 30.600 143.988   4045
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.85 %
    Favored  : 79.10 %
  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 are not related in a simple way.
  whole:  2.59 (0.31), residues: 732
  helix:  2.39 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.46 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  71 
 TYR   0.010   0.001   TYR D  40 
 PHE   0.010   0.002   PHE G  25 
 HIS   0.002   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (12771)
  covalent geometry    : angle       0.55530 (18509)
  hydrogen bonds       : bond        0.04070 (  775)
  hydrogen bonds       : angle       2.82821 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7914 (mtp85)
REVERT: B   77 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8764 (mtpt)
REVERT: C   64 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8295 (tt0)
REVERT: C   95 LYS cc_start: 0.9201 (ttpp) cc_final: 0.8951 (ttpp)
REVERT: E  120 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7719 (mtt)
REVERT: G   64 GLU cc_start: 0.8689 (tt0) cc_final: 0.8325 (tp30)
REVERT: G   91 GLU cc_start: 0.8691 (tp30) cc_final: 0.8452 (tp30)
REVERT: H   63 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8671 (m-40)
  outliers start: 19
  outliers final: 6
  residues processed: 163
  average time/residue: 0.8739
  time to fit residues: 150.0206
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.099120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.066289 restraints weight = 21522.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.51
r_work: 0.2734 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12771  Z= 0.165
  Angle     :  0.547   7.340  18509  Z= 0.332
  Chirality :  0.033   0.137   2108
  Planarity :  0.004   0.042   1322
  Dihedral  : 30.636 144.350   4045
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.81 %
    Favored  : 78.62 %
  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 are not related in a simple way.
  whole:  2.75 (0.31), residues: 732
  helix:  2.50 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.37 (0.44), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  71 
 TYR   0.015   0.001   TYR D  42 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12771)
  covalent geometry    : angle       0.54660 (18509)
  hydrogen bonds       : bond        0.03761 (  775)
  hydrogen bonds       : angle       2.83717 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8242 (ttt90) cc_final: 0.7911 (mtp85)
REVERT: A  120 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7724 (mtt)
REVERT: B   77 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8760 (mtpt)
REVERT: C   64 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (tt0)
REVERT: C   95 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8932 (ttpp)
REVERT: G   64 GLU cc_start: 0.8666 (tt0) cc_final: 0.8303 (tp30)
REVERT: G   91 GLU cc_start: 0.8666 (tp30) cc_final: 0.8414 (tp30)
REVERT: H   63 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8613 (m-40)
  outliers start: 16
  outliers final: 7
  residues processed: 161
  average time/residue: 0.8664
  time to fit residues: 146.9642
Evaluate side-chains
  168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 157
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.096734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.063313 restraints weight = 21551.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 1.52
r_work: 0.2666 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  12771  Z= 0.304
  Angle     :  0.597   5.527  18509  Z= 0.358
  Chirality :  0.038   0.171   2108
  Planarity :  0.004   0.048   1322
  Dihedral  : 31.007 146.261   4045
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.45 %
    Favored  : 77.81 %
  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 are not related in a simple way.
  whole:  2.54 (0.31), residues: 732
  helix:  2.39 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.58 (0.42), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  23 
 TYR   0.012   0.002   TYR H  42 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.003   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (12771)
  covalent geometry    : angle       0.59715 (18509)
  hydrogen bonds       : bond        0.04476 (  775)
  hydrogen bonds       : angle       2.88279 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7901 (mtp85)
REVERT: B   77 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8762 (mtpt)
REVERT: B   79 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8606 (mtmp)
REVERT: C   64 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8276 (tt0)
REVERT: C   75 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8829 (mttm)
REVERT: C   95 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8866 (ttpp)
REVERT: E   59 GLU cc_start: 0.8711 (pt0) cc_final: 0.8407 (pm20)
REVERT: G   91 GLU cc_start: 0.8665 (tp30) cc_final: 0.8374 (tp30)
REVERT: H   63 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8734 (m-40)
  outliers start: 17
  outliers final: 8
  residues processed: 162
  average time/residue: 0.9226
  time to fit residues: 157.1206
Evaluate side-chains
  167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.097985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.064621 restraints weight = 21405.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.51
r_work: 0.2691 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2548 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12771  Z= 0.168
  Angle     :  0.564   5.942  18509  Z= 0.342
  Chirality :  0.034   0.135   2108
  Planarity :  0.004   0.048   1322
  Dihedral  : 31.028 146.346   4045
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.77 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.73 (0.31), residues: 732
  helix:  2.53 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.44 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  71 
 TYR   0.012   0.001   TYR D  42 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12771)
  covalent geometry    : angle       0.56416 (18509)
  hydrogen bonds       : bond        0.03889 (  775)
  hydrogen bonds       : angle       2.83680 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7943 (mtp85)
REVERT: B   77 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8771 (mtpt)
REVERT: B   79 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8641 (mtmp)
REVERT: C   64 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8283 (tt0)
REVERT: C   75 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (mttm)
REVERT: C   95 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8937 (ttpp)
REVERT: E   59 GLU cc_start: 0.8668 (pt0) cc_final: 0.8400 (pm20)
REVERT: G   64 GLU cc_start: 0.8700 (tt0) cc_final: 0.8346 (tp30)
REVERT: G   91 GLU cc_start: 0.8654 (tp30) cc_final: 0.8365 (tp30)
REVERT: H   63 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8736 (m-40)
REVERT: H   99 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8748 (mtm-85)
  outliers start: 16
  outliers final: 7
  residues processed: 161
  average time/residue: 0.8689
  time to fit residues: 147.4842
Evaluate side-chains
  167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.097903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.064653 restraints weight = 21481.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.51
r_work: 0.2694 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  12771  Z= 0.220
  Angle     :  0.560   5.934  18509  Z= 0.339
  Chirality :  0.035   0.141   2108
  Planarity :  0.004   0.048   1322
  Dihedral  : 30.876 144.692   4045
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.42 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.31), residues: 732
  helix:  2.57 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.51 (0.43), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  71 
 TYR   0.010   0.001   TYR H  42 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (12771)
  covalent geometry    : angle       0.55983 (18509)
  hydrogen bonds       : bond        0.03766 (  775)
  hydrogen bonds       : angle       2.78051 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7951 (mtp85)
REVERT: B   77 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8788 (mtpt)
REVERT: C   64 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8285 (tt0)
REVERT: C   75 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8847 (mttm)
REVERT: C   95 LYS cc_start: 0.9221 (ttpp) cc_final: 0.8920 (ttpp)
REVERT: E   59 GLU cc_start: 0.8641 (pt0) cc_final: 0.8385 (pm20)
REVERT: G   64 GLU cc_start: 0.8706 (tt0) cc_final: 0.8368 (tp30)
REVERT: G   91 GLU cc_start: 0.8652 (tp30) cc_final: 0.8379 (tp30)
REVERT: H   63 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8740 (m-40)
  outliers start: 14
  outliers final: 6
  residues processed: 162
  average time/residue: 0.8888
  time to fit residues: 151.5598
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.097536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.064838 restraints weight = 21545.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 1.48
r_work: 0.2712 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2574 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12771  Z= 0.234
  Angle     :  0.573   6.582  18509  Z= 0.345
  Chirality :  0.035   0.171   2108
  Planarity :  0.004   0.050   1322
  Dihedral  : 30.910 144.887   4045
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.06 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.31), residues: 732
  helix:  2.54 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.50 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  71 
 TYR   0.010   0.001   TYR H  42 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.002   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (12771)
  covalent geometry    : angle       0.57301 (18509)
  hydrogen bonds       : bond        0.03878 (  775)
  hydrogen bonds       : angle       2.79597 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8253 (ttt90) cc_final: 0.7926 (mtp85)
REVERT: B   77 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8787 (mtpt)
REVERT: C   64 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (tt0)
REVERT: C   75 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8828 (mttm)
REVERT: C   95 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8914 (ttpp)
REVERT: E   59 GLU cc_start: 0.8661 (pt0) cc_final: 0.8402 (pm20)
REVERT: G   64 GLU cc_start: 0.8688 (tt0) cc_final: 0.8350 (tp30)
REVERT: G   91 GLU cc_start: 0.8635 (tp30) cc_final: 0.8361 (tp30)
REVERT: H   63 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8737 (m-40)
  outliers start: 10
  outliers final: 7
  residues processed: 159
  average time/residue: 0.8764
  time to fit residues: 146.6134
Evaluate side-chains
  164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.098777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.065622 restraints weight = 21468.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.51
r_work: 0.2711 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12771  Z= 0.172
  Angle     :  0.553   6.715  18509  Z= 0.335
  Chirality :  0.033   0.145   2108
  Planarity :  0.004   0.051   1322
  Dihedral  : 30.852 144.357   4045
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.90 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.31), residues: 732
  helix:  2.63 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.44 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  71 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12771)
  covalent geometry    : angle       0.55329 (18509)
  hydrogen bonds       : bond        0.03450 (  775)
  hydrogen bonds       : angle       2.74276 ( 1931)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7899 (mtp85)
REVERT: B   77 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8755 (mtpt)
REVERT: C   64 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8224 (tt0)
REVERT: C   75 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8769 (mttm)
REVERT: C   95 LYS cc_start: 0.9189 (ttpp) cc_final: 0.8912 (ttpp)
REVERT: E   59 GLU cc_start: 0.8578 (pt0) cc_final: 0.8287 (pm20)
REVERT: G   64 GLU cc_start: 0.8673 (tt0) cc_final: 0.8325 (tp30)
REVERT: G   91 GLU cc_start: 0.8630 (tp30) cc_final: 0.8344 (tp30)
REVERT: H   63 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8665 (m-40)
  outliers start: 11
  outliers final: 7
  residues processed: 163
  average time/residue: 0.8683
  time to fit residues: 149.0861
Evaluate side-chains
  167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.098860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.065752 restraints weight = 21367.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.51
r_work: 0.2718 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2577 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12771  Z= 0.164
  Angle     :  0.559   6.739  18509  Z= 0.336
  Chirality :  0.033   0.172   2108
  Planarity :  0.004   0.051   1322
  Dihedral  : 30.832 144.193   4045
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.74 %
    Favored  : 77.49 %
  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 are not related in a simple way.
  whole:  2.88 (0.31), residues: 732
  helix:  2.65 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.40 (0.44), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  71 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12771)
  covalent geometry    : angle       0.55866 (18509)
  hydrogen bonds       : bond        0.03391 (  775)
  hydrogen bonds       : angle       2.74151 ( 1931)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4371.41 seconds
wall clock time: 74 minutes 44.36 seconds (4484.36 seconds total)