Starting phenix.real_space_refine
on Wed Mar  4 06:30:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6px1_20516/03_2026/6px1_20516.map"
  }
  resolution = 3.3
  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=   0.007
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     290      5.49       5
     S      12      5.16       5
     C    6594      2.51       5
     N    2249      2.21       5
     O    2792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11937
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    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: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 792
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 752
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, '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: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 792
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 752
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.96, per 1000 atoms: 0.25
  Number of scatterers: 11937
  At special positions: 0
  Unit cell: (73.84, 117.52, 114.4, 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      12     16.00
     P     290     15.00
     O    2792      8.00
     N    2249      7.00
     C    6594      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 386.2 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      70.9% alpha, 3.2% beta
      143 base pairs and 274 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.672A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASP A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.668A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.578A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.613A  pdb=" N   ILE C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.553A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 102 through 120
      removed outlier: 3.835A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.694A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
    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: 3.764A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'G' and resid 17 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.339A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE G  62 " --> pdb=" O   LEU G  58 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.530A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.612A  pdb=" N   LEU G 116 " --> pdb=" O   SER G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.521A  pdb=" N   ARG H  76 " --> pdb=" O   GLY H  72 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 102 through 120
      removed outlier: 3.863A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.765A  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: 6.412A  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: 7.154A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.904A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.272A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    376 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      274 stacking parallelities
  Total time for adding SS restraints: 2.35

  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: 2040
        1.33 -     1.45: 4253
        1.45 -     1.57: 5847
        1.57 -     1.68: 578
        1.68 -     1.80: 22
  Bond restraints: 12740
  Sorted by residual:
  bond pdb=" C3'  DG J  94 "
       pdb=" O3'  DG J  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.12e+00
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.10e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.485 -0.063 3.00e-02 1.11e+03 4.40e+00
  bond pdb=" CG1 ILE D  58 "
       pdb=" CD1 ILE D  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.437  0.076 3.90e-02 6.57e+02 3.79e+00
  bond pdb=" CG1 ILE H  58 "
       pdb=" CD1 ILE H  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.439  0.074 3.90e-02 6.57e+02 3.64e+00
  ... (remaining 12735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 17527
        1.85 -     3.70: 853
        3.70 -     5.55: 44
        5.55 -     7.40: 19
        7.40 -     9.25: 4
  Bond angle restraints: 18447
  Sorted by residual:
  angle pdb=" C   GLU G  64 "
        pdb=" CA  GLU G  64 "
        pdb=" CB  GLU G  64 "
      ideal   model   delta    sigma   weight residual
     110.90  102.08    8.82 1.58e+00 4.01e-01 3.12e+01
  angle pdb=" N   GLU D  32 "
        pdb=" CA  GLU D  32 "
        pdb=" C   GLU D  32 "
      ideal   model   delta    sigma   weight residual
     108.58  117.83   -9.25 1.82e+00 3.02e-01 2.58e+01
  angle pdb=" C3'  DC J 126 "
        pdb=" O3'  DC J 126 "
        pdb=" P    DC J 127 "
      ideal   model   delta    sigma   weight residual
     120.20  126.32   -6.12 1.50e+00 4.44e-01 1.66e+01
  angle pdb=" C3'  DG J  94 "
        pdb=" O3'  DG J  94 "
        pdb=" P    DG J  95 "
      ideal   model   delta    sigma   weight residual
     120.20  126.09   -5.89 1.50e+00 4.44e-01 1.54e+01
  angle pdb=" N   ARG D  30 "
        pdb=" CA  ARG D  30 "
        pdb=" C   ARG D  30 "
      ideal   model   delta    sigma   weight residual
     109.71  114.76   -5.05 1.41e+00 5.03e-01 1.28e+01
  ... (remaining 18442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 5436
       35.51 -    71.02: 1476
       71.02 -   106.54: 5
      106.54 -   142.05: 0
      142.05 -   177.56: 3
  Dihedral angle restraints: 6920
    sinusoidal: 4738
      harmonic: 2182
  Sorted by residual:
  dihedral pdb=" CA  PRO G 117 "
           pdb=" C   PRO G 117 "
           pdb=" N   LYS G 118 "
           pdb=" CA  LYS G 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.87  -25.13     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  LYS D  31 "
           pdb=" C   LYS D  31 "
           pdb=" N   GLU D  32 "
           pdb=" CA  GLU D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.56 -177.56     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 6917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1618
       0.056 -    0.112: 410
       0.112 -    0.168: 56
       0.168 -    0.224: 11
       0.224 -    0.280: 3
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  THR A  45 "
            pdb=" N   THR A  45 "
            pdb=" C   THR A  45 "
            pdb=" CB  THR A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" C3'  DC J 126 "
            pdb=" C4'  DC J 126 "
            pdb=" O3'  DC J 126 "
            pdb=" C2'  DC J 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.44   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  68 "   -0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        pdb=" C   GLU D  68 "    0.076 2.00e-02 2.50e+03
        pdb=" O   GLU D  68 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG D  69 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F  64 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   ASN F  64 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASN F  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL F  65 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F  80 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   THR F  80 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   THR F  80 "    0.019 2.00e-02 2.50e+03
        pdb=" N   VAL F  81 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1790
        2.76 -     3.30: 9452
        3.30 -     3.83: 23879
        3.83 -     4.37: 28890
        4.37 -     4.90: 40918
  Nonbonded interactions: 104929
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OE1 GLN F  93 "
            pdb=" NH2 ARG F  95 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.329 3.040
  ... (remaining 104924 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'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.250
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.230
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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      :  0.006   0.076  12740  Z= 0.270
  Angle     :  0.867   9.252  18447  Z= 0.524
  Chirality :  0.050   0.280   2098
  Planarity :  0.008   0.068   1330
  Dihedral  : 28.550 177.562   5512
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.24), residues: 736
  helix: -1.77 (0.18), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.02 (0.34), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F  95 
 TYR   0.024   0.003   TYR E  41 
 PHE   0.019   0.003   PHE C  25 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 (12740)
  covalent geometry    : angle       0.86723 (18447)
  hydrogen bonds       : bond        0.09859 (  744)
  hydrogen bonds       : angle       4.03200 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.311 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8710 (m-40) cc_final: 0.8490 (m-40)
REVERT: F   35 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8052 (mtm110)
REVERT: G   42 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.8052 (mtm180)
REVERT: G   94 ASN cc_start: 0.8629 (t0) cc_final: 0.8325 (t0)
REVERT: H   87 THR cc_start: 0.8363 (p) cc_final: 0.8142 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2225
  time to fit residues: 44.8386
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
D  92 GLN
E  68 GLN
E 113 HIS
F  25 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.144558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.101419 restraints weight = 17049.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.50
r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12740  Z= 0.165
  Angle     :  0.589  10.052  18447  Z= 0.353
  Chirality :  0.034   0.181   2098
  Planarity :  0.005   0.058   1330
  Dihedral  : 31.068 174.294   4008
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.63 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.29), residues: 736
  helix:  0.13 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.46 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  92 
 TYR   0.009   0.001   TYR D  37 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12740)
  covalent geometry    : angle       0.58940 (18447)
  hydrogen bonds       : bond        0.03751 (  744)
  hydrogen bonds       : angle       2.88986 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.325 
Fit side-chains
REVERT: B   72 TYR cc_start: 0.8974 (m-80) cc_final: 0.8681 (m-80)
REVERT: E   59 GLU cc_start: 0.8010 (mp0) cc_final: 0.7715 (mp0)
REVERT: E   73 GLU cc_start: 0.7832 (tt0) cc_final: 0.7580 (tt0)
REVERT: F   25 ASN cc_start: 0.8814 (m110) cc_final: 0.8592 (m-40)
REVERT: G   42 ARG cc_start: 0.8337 (ptp-170) cc_final: 0.7967 (mtm180)
  outliers start: 5
  outliers final: 2
  residues processed: 138
  average time/residue: 0.1813
  time to fit residues: 31.9134
Evaluate side-chains
  132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  75 HIS
C  68 ASN
C  73 ASN
D  81 ASN
D  92 GLN
E  76 GLN
F  75 HIS
G 104 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.142210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.099154 restraints weight = 17291.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.47
r_work: 0.3083 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12740  Z= 0.205
  Angle     :  0.585  10.509  18447  Z= 0.349
  Chirality :  0.036   0.175   2098
  Planarity :  0.005   0.050   1330
  Dihedral  : 31.079 172.397   4008
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.54 %
    Favored  : 86.03 %
  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:  0.73 (0.30), residues: 736
  helix:  1.07 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -1.04 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  77 
 TYR   0.010   0.001   TYR D  34 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (12740)
  covalent geometry    : angle       0.58503 (18447)
  hydrogen bonds       : bond        0.03788 (  744)
  hydrogen bonds       : angle       2.71533 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7744 (pm20)
REVERT: A  133 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: B   72 TYR cc_start: 0.8957 (m-80) cc_final: 0.8729 (m-80)
REVERT: D   83 ARG cc_start: 0.8452 (mmt-90) cc_final: 0.8249 (mmt90)
REVERT: E   59 GLU cc_start: 0.8115 (mp0) cc_final: 0.7861 (mp0)
REVERT: E   73 GLU cc_start: 0.7795 (tt0) cc_final: 0.7519 (tt0)
REVERT: F   25 ASN cc_start: 0.8764 (m110) cc_final: 0.8549 (m-40)
REVERT: F   85 ASP cc_start: 0.8453 (m-30) cc_final: 0.8137 (m-30)
REVERT: G   42 ARG cc_start: 0.8353 (ptp-170) cc_final: 0.7973 (mtm180)
REVERT: H   54 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8287 (mmtt)
  outliers start: 9
  outliers final: 8
  residues processed: 133
  average time/residue: 0.1691
  time to fit residues: 28.6974
Evaluate side-chains
  132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  92 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.143563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.100577 restraints weight = 17204.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.46
r_work: 0.3096 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12740  Z= 0.164
  Angle     :  0.547   9.639  18447  Z= 0.330
  Chirality :  0.033   0.167   2098
  Planarity :  0.004   0.047   1330
  Dihedral  : 30.912 174.525   4008
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.33 %
    Favored  : 85.24 %
  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:  1.45 (0.31), residues: 736
  helix:  1.61 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.83 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  76 
 TYR   0.009   0.001   TYR D 118 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12740)
  covalent geometry    : angle       0.54697 (18447)
  hydrogen bonds       : bond        0.03351 (  744)
  hydrogen bonds       : angle       2.59559 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8085 (ttpp)
REVERT: A   59 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7803 (pm20)
REVERT: A  133 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: D   49 THR cc_start: 0.8988 (m) cc_final: 0.8742 (t)
REVERT: E   73 GLU cc_start: 0.7760 (tt0) cc_final: 0.7470 (tt0)
REVERT: F   25 ASN cc_start: 0.8739 (m110) cc_final: 0.8530 (m-40)
REVERT: F   85 ASP cc_start: 0.8348 (m-30) cc_final: 0.8021 (m-30)
REVERT: G   42 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.7941 (mtm180)
REVERT: H   90 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7897 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1639
  time to fit residues: 26.6978
Evaluate side-chains
  123 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0000
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.5590

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

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN
E  76 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.142964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099747 restraints weight = 17576.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.45
r_work: 0.3103 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12740  Z= 0.188
  Angle     :  0.558  10.478  18447  Z= 0.334
  Chirality :  0.034   0.164   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 30.954 175.618   4008
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.49 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.31), residues: 736
  helix:  1.82 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.81 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  83 
 TYR   0.017   0.001   TYR D 118 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (12740)
  covalent geometry    : angle       0.55844 (18447)
  hydrogen bonds       : bond        0.03524 (  744)
  hydrogen bonds       : angle       2.59909 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8137 (ttpp)
REVERT: A   59 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7863 (pm20)
REVERT: C   24 GLN cc_start: 0.8662 (mm110) cc_final: 0.8326 (mm110)
REVERT: D   37 TYR cc_start: 0.9168 (m-80) cc_final: 0.8599 (m-80)
REVERT: D   49 THR cc_start: 0.8997 (m) cc_final: 0.8752 (t)
REVERT: D   90 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7899 (mp0)
REVERT: E   59 GLU cc_start: 0.8040 (mp0) cc_final: 0.7645 (pm20)
REVERT: E   73 GLU cc_start: 0.7831 (tt0) cc_final: 0.7530 (tt0)
REVERT: F   25 ASN cc_start: 0.8773 (m110) cc_final: 0.8505 (m-40)
REVERT: F   85 ASP cc_start: 0.8384 (m-30) cc_final: 0.8089 (m-30)
REVERT: G   42 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.7968 (mtm180)
REVERT: H   54 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8339 (mmtt)
REVERT: H   90 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7875 (mp0)
REVERT: H  113 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8400 (ttpp)
  outliers start: 14
  outliers final: 11
  residues processed: 126
  average time/residue: 0.1403
  time to fit residues: 23.5645
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 89 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.143657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.101375 restraints weight = 17671.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.42
r_work: 0.3137 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12740  Z= 0.150
  Angle     :  0.539  10.375  18447  Z= 0.323
  Chirality :  0.033   0.159   2098
  Planarity :  0.004   0.046   1330
  Dihedral  : 30.747 177.223   4008
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.60 %
    Favored  : 83.49 %
  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:  2.12 (0.31), residues: 736
  helix:  2.15 (0.23), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.70 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  77 
 TYR   0.016   0.001   TYR D 118 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (12740)
  covalent geometry    : angle       0.53917 (18447)
  hydrogen bonds       : bond        0.03278 (  744)
  hydrogen bonds       : angle       2.53207 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7495 (mt-10)
REVERT: B   92 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8617 (ptm-80)
REVERT: C   24 GLN cc_start: 0.8540 (mm110) cc_final: 0.8112 (mm-40)
REVERT: D   37 TYR cc_start: 0.9148 (m-80) cc_final: 0.8576 (m-80)
REVERT: D   49 THR cc_start: 0.8994 (m) cc_final: 0.8766 (t)
REVERT: D   90 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7842 (mp0)
REVERT: E   59 GLU cc_start: 0.7922 (mp0) cc_final: 0.7598 (pm20)
REVERT: E   73 GLU cc_start: 0.7908 (tt0) cc_final: 0.7616 (tt0)
REVERT: F   25 ASN cc_start: 0.8726 (m110) cc_final: 0.8485 (m-40)
REVERT: F   85 ASP cc_start: 0.8313 (m-30) cc_final: 0.8006 (m-30)
REVERT: G   42 ARG cc_start: 0.8300 (ptp-170) cc_final: 0.7958 (mtm180)
REVERT: H   90 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7909 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 124
  average time/residue: 0.1466
  time to fit residues: 24.2151
Evaluate side-chains
  124 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.144653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102077 restraints weight = 17653.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.42
r_work: 0.3151 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12740  Z= 0.150
  Angle     :  0.542  10.967  18447  Z= 0.324
  Chirality :  0.033   0.155   2098
  Planarity :  0.004   0.046   1330
  Dihedral  : 30.689 178.001   4008
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.29 %
    Favored  : 83.81 %
  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:  2.43 (0.31), residues: 736
  helix:  2.40 (0.23), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.59 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.016   0.001   TYR D 118 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (12740)
  covalent geometry    : angle       0.54199 (18447)
  hydrogen bonds       : bond        0.03281 (  744)
  hydrogen bonds       : angle       2.48051 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7460 (mt-10)
REVERT: B   92 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8607 (ptm-80)
REVERT: C   24 GLN cc_start: 0.8523 (mm110) cc_final: 0.8098 (mm110)
REVERT: D   37 TYR cc_start: 0.9144 (m-80) cc_final: 0.8581 (m-80)
REVERT: D   49 THR cc_start: 0.9001 (m) cc_final: 0.8765 (t)
REVERT: D   90 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7864 (mp0)
REVERT: E   59 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7616 (pm20)
REVERT: E   73 GLU cc_start: 0.7918 (tt0) cc_final: 0.7613 (tt0)
REVERT: F   25 ASN cc_start: 0.8716 (m110) cc_final: 0.8451 (m-40)
REVERT: F   85 ASP cc_start: 0.8254 (m-30) cc_final: 0.7939 (m-30)
REVERT: G   42 ARG cc_start: 0.8317 (ptp-170) cc_final: 0.7964 (mtm180)
REVERT: H   43 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8433 (mmtt)
REVERT: H   54 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8304 (mmtt)
REVERT: H   90 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7943 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 127
  average time/residue: 0.1595
  time to fit residues: 26.6105
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 88 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 4 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  24 GLN
D  44 GLN
E  76 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.142001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.099539 restraints weight = 17802.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.44
r_work: 0.3116 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12740  Z= 0.184
  Angle     :  0.557  11.663  18447  Z= 0.329
  Chirality :  0.034   0.157   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 30.897 178.157   4008
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.81 %
    Favored  : 83.49 %
  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:  2.30 (0.31), residues: 736
  helix:  2.31 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.57 (0.40), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  39 
 TYR   0.019   0.001   TYR D 118 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (12740)
  covalent geometry    : angle       0.55733 (18447)
  hydrogen bonds       : bond        0.03551 (  744)
  hydrogen bonds       : angle       2.55116 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.278 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8595 (ptm-80)
REVERT: C   24 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8273 (mm-40)
REVERT: D   49 THR cc_start: 0.9018 (m) cc_final: 0.8774 (t)
REVERT: D   90 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7876 (mp0)
REVERT: E   59 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7673 (pm20)
REVERT: E   73 GLU cc_start: 0.7865 (tt0) cc_final: 0.7608 (tt0)
REVERT: F   25 ASN cc_start: 0.8697 (m110) cc_final: 0.8176 (m-40)
REVERT: F   85 ASP cc_start: 0.8256 (m-30) cc_final: 0.7939 (m-30)
REVERT: G   42 ARG cc_start: 0.8337 (ptp-170) cc_final: 0.7920 (mtm180)
REVERT: H   54 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8304 (mmtt)
REVERT: H   90 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7884 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 131
  average time/residue: 0.1645
  time to fit residues: 28.0684
Evaluate side-chains
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.144021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.101217 restraints weight = 17750.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.43
r_work: 0.3137 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12740  Z= 0.162
  Angle     :  0.547  11.958  18447  Z= 0.324
  Chirality :  0.033   0.154   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 30.797 178.606   4008
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.44 %
    Favored  : 83.17 %
  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:  2.46 (0.31), residues: 736
  helix:  2.43 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.51 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  39 
 TYR   0.016   0.001   TYR D 118 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12740)
  covalent geometry    : angle       0.54669 (18447)
  hydrogen bonds       : bond        0.03407 (  744)
  hydrogen bonds       : angle       2.52553 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7618 (mt-10)
REVERT: B   92 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8589 (ptm-80)
REVERT: D   49 THR cc_start: 0.9008 (m) cc_final: 0.8788 (t)
REVERT: D   90 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7870 (mp0)
REVERT: E   59 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7701 (pm20)
REVERT: E   73 GLU cc_start: 0.7849 (tt0) cc_final: 0.7483 (tt0)
REVERT: F   25 ASN cc_start: 0.8712 (m110) cc_final: 0.8440 (m-40)
REVERT: F   85 ASP cc_start: 0.8225 (m-30) cc_final: 0.7897 (m-30)
REVERT: G   42 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7933 (mtm180)
REVERT: H   43 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8603 (mmtt)
REVERT: H   54 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8294 (mmtt)
REVERT: H   90 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7864 (mp0)
  outliers start: 15
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1540
  time to fit residues: 25.5167
Evaluate side-chains
  132 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.145332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.102350 restraints weight = 17641.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.43
r_work: 0.3148 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12740  Z= 0.149
  Angle     :  0.546  12.449  18447  Z= 0.322
  Chirality :  0.033   0.152   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 30.734 179.022   4008
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.24 %
    Favored  : 82.86 %
  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:  2.58 (0.31), residues: 736
  helix:  2.48 (0.23), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.41 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  39 
 TYR   0.017   0.001   TYR D 118 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (12740)
  covalent geometry    : angle       0.54600 (18447)
  hydrogen bonds       : bond        0.03334 (  744)
  hydrogen bonds       : angle       2.50324 ( 1849)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   90 MET cc_start: 0.8475 (tpp) cc_final: 0.8158 (mmp)
REVERT: A  133 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7715 (mt-10)
REVERT: B   92 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8542 (ptm-80)
REVERT: D   49 THR cc_start: 0.9003 (m) cc_final: 0.8771 (t)
REVERT: D   56 MET cc_start: 0.8879 (tpp) cc_final: 0.8417 (tpt)
REVERT: D   90 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7831 (mp0)
REVERT: E   59 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7733 (pm20)
REVERT: E   73 GLU cc_start: 0.7825 (tt0) cc_final: 0.7476 (tt0)
REVERT: F   25 ASN cc_start: 0.8693 (m110) cc_final: 0.8430 (m-40)
REVERT: F   85 ASP cc_start: 0.8213 (m-30) cc_final: 0.7884 (m-30)
REVERT: G   42 ARG cc_start: 0.8326 (ptp-170) cc_final: 0.7902 (mtm180)
REVERT: H   43 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8553 (mmtt)
REVERT: H   54 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8291 (mmtt)
REVERT: H   56 MET cc_start: 0.8856 (tpp) cc_final: 0.8365 (tpt)
  outliers start: 12
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1638
  time to fit residues: 26.1123
Evaluate side-chains
  128 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 55 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.145898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.102996 restraints weight = 17703.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.43
r_work: 0.3151 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
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      :  0.003   0.043  12740  Z= 0.143
  Angle     :  0.542  12.553  18447  Z= 0.320
  Chirality :  0.033   0.151   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 30.662 179.407   4008
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.71 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.31), residues: 736
  helix:  2.56 (0.23), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.37 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  83 
 TYR   0.016   0.001   TYR D 118 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12740)
  covalent geometry    : angle       0.54167 (18447)
  hydrogen bonds       : bond        0.03300 (  744)
  hydrogen bonds       : angle       2.49300 ( 1849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2437.92 seconds
wall clock time: 42 minutes 24.61 seconds (2544.61 seconds total)