Starting phenix.real_space_refine
on Wed Mar  4 02:55:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d69_30591/03_2026/7d69_30591.cif"
  }
  resolution = 3.57
  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=   1.000
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     250      5.49       5
     S      13      5.16       5
     C    6015      2.51       5
     N    2012      2.21       5
     O    2567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 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: 10857
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 716
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 779
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 621
          Classifications: {'peptide': 78}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "G"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2561
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2564
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
  Time building chain proxies: 2.47, per 1000 atoms: 0.23
  Number of scatterers: 10857
  At special positions: 0
  Unit cell: (84, 121.8, 114.45, 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      13     16.00
     P     250     15.00
     O    2567      8.00
     N    2012      7.00
     C    6015      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: 0.86
  Conformation dependent library (CDL) restraints added in 318.6 milliseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      74.0% alpha, 1.9% beta
      121 base pairs and 227 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 58
      removed outlier: 3.897A  pdb=" N   TYR A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 78
    Processing helix  chain 'A' and resid 88 through 117
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 26 through 37
    Processing helix  chain 'B' and resid 45 through 72
      removed outlier: 3.698A  pdb=" N   GLY B  72 " --> pdb=" O   TYR B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 90
    Processing helix  chain 'D' and resid 30 through 45
      removed outlier: 3.607A  pdb=" N   ILE D  43 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ARG D  44 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 84
    Processing helix  chain 'D' and resid 89 through 101
    Processing helix  chain 'D' and resid 103 through 122
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 4.096A  pdb=" N   VAL E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS E  50 " --> pdb=" O   MET E  46 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER E  58 " --> pdb=" O   LYS E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 79
    Processing helix  chain 'E' and resid 88 through 117
    Processing helix  chain 'E' and resid 123 through 133
    Processing helix  chain 'F' and resid 21 through 25
    Processing helix  chain 'F' and resid 26 through 38
    Processing helix  chain 'F' and resid 44 through 72
      removed outlier: 4.273A  pdb=" N   GLN F  48 " --> pdb=" O   SER F  44 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY F  72 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 88
    Processing helix  chain 'H' and resid 30 through 43
    Processing helix  chain 'H' and resid 54 through 84
    Processing helix  chain 'H' and resid 89 through 101
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'C' and resid 13 through 18
    Processing helix  chain 'C' and resid 23 through 34
    Processing helix  chain 'C' and resid 42 through 68
      removed outlier: 4.162A  pdb=" N   VAL C  46 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 87
      removed outlier: 3.604A  pdb=" N   ASP C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 94
    Processing helix  chain 'G' and resid 13 through 18
    Processing helix  chain 'G' and resid 23 through 34
    Processing helix  chain 'G' and resid 43 through 68
      removed outlier: 3.618A  pdb=" N   TYR G  47 " --> pdb=" O   ASP G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 76 through 87
      removed outlier: 4.103A  pdb=" N   ASP G  87 " --> pdb=" O   ALA G  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 7.028A  pdb=" N   ARG A  86 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122
    Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94
      removed outlier: 3.681A  pdb=" N   TYR B  94 " --> pdb=" O   THR G  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87
      removed outlier: 7.127A  pdb=" N   ARG E  86 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122
    Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94
      removed outlier: 6.189A  pdb=" N   THR F  92 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    392 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      315 hydrogen bonds
      630 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      227 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.13 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: 1840
        1.33 -     1.45: 3827
        1.45 -     1.57: 5355
        1.57 -     1.68: 498
        1.68 -     1.80: 22
  Bond restraints: 11542
  Sorted by residual:
  bond pdb=" CG1 ILE G  24 "
       pdb=" CD1 ILE G  24 "
    ideal  model  delta    sigma   weight residual
    1.513  1.430  0.083 3.90e-02 6.57e+02 4.50e+00
  bond pdb=" CG  GLN B  89 "
       pdb=" CD  GLN B  89 "
    ideal  model  delta    sigma   weight residual
    1.516  1.473  0.043 2.50e-02 1.60e+03 2.89e+00
  bond pdb=" CB  VAL A  76 "
       pdb=" CG1 VAL A  76 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CG  LEU F  86 "
       pdb=" CD1 LEU F  86 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  bond pdb=" CB  VAL D  37 "
       pdb=" CG1 VAL D  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 15163
        1.54 -     3.07: 1325
        3.07 -     4.61: 121
        4.61 -     6.14: 19
        6.14 -     7.68: 9
  Bond angle restraints: 16637
  Sorted by residual:
  angle pdb=" C3'  DT J 114 "
        pdb=" O3'  DT J 114 "
        pdb=" P    DC J 115 "
      ideal   model   delta    sigma   weight residual
     120.20  125.46   -5.26 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" C3'  DT I 120 "
        pdb=" O3'  DT I 120 "
        pdb=" P    DC I 121 "
      ideal   model   delta    sigma   weight residual
     120.20  124.81   -4.61 1.50e+00 4.44e-01 9.45e+00
  angle pdb=" O4'  DA I 113 "
        pdb=" C1'  DA I 113 "
        pdb=" N9   DA I 113 "
      ideal   model   delta    sigma   weight residual
     108.40  104.02    4.38 1.50e+00 4.44e-01 8.51e+00
  angle pdb=" C4'  DA I  72 "
        pdb=" C3'  DA I  72 "
        pdb=" O3'  DA I  72 "
      ideal   model   delta    sigma   weight residual
     110.00  105.80    4.20 1.50e+00 4.44e-01 7.83e+00
  angle pdb=" O4'  DG J  11 "
        pdb=" C1'  DG J  11 "
        pdb=" C2'  DG J  11 "
      ideal   model   delta    sigma   weight residual
     106.40  102.23    4.17 1.50e+00 4.44e-01 7.72e+00
  ... (remaining 16632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.69: 4776
       30.69 -    61.37: 1489
       61.37 -    92.05: 46
       92.05 -   122.74: 8
      122.74 -   153.42: 4
  Dihedral angle restraints: 6323
    sinusoidal: 4214
      harmonic: 2109
  Sorted by residual:
  dihedral pdb=" C4'  DT I 120 "
           pdb=" C3'  DT I 120 "
           pdb=" O3'  DT I 120 "
           pdb=" P    DC I 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.58  153.42     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" C4'  DT J 114 "
           pdb=" C3'  DT J 114 "
           pdb=" O3'  DT J 114 "
           pdb=" P    DC J 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.89  143.11     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" C4'  DC I 100 "
           pdb=" C3'  DC I 100 "
           pdb=" O3'  DC I 100 "
           pdb=" P    DT I 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   94.95  125.05     1      3.50e+01 8.16e-04 1.23e+01
  ... (remaining 6320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1230
       0.048 -    0.095: 510
       0.095 -    0.143: 142
       0.143 -    0.190: 19
       0.190 -    0.237: 1
  Chirality restraints: 1902
  Sorted by residual:
  chirality pdb=" C3'  DT J 114 "
            pdb=" C4'  DT J 114 "
            pdb=" O3'  DT J 114 "
            pdb=" C2'  DT J 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  THR G  98 "
            pdb=" CA  THR G  98 "
            pdb=" OG1 THR G  98 "
            pdb=" CG2 THR G  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.63e-01
  chirality pdb=" C4'  DA I  83 "
            pdb=" C5'  DA I  83 "
            pdb=" O4'  DA I  83 "
            pdb=" C3'  DA I  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.34   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 1899 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   9 "   -0.036 2.00e-02 2.50e+03   1.88e-02 7.92e+00
        pdb=" N1   DC I   9 "    0.039 2.00e-02 2.50e+03
        pdb=" C2   DC I   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2   DC I   9 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I   9 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC I   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I   9 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J   9 "   -0.024 2.00e-02 2.50e+03   1.78e-02 7.11e+00
        pdb=" N1   DC J   9 "    0.044 2.00e-02 2.50e+03
        pdb=" C2   DC J   9 "   -0.017 2.00e-02 2.50e+03
        pdb=" O2   DC J   9 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DC J   9 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DC J   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J   9 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  31 "   -0.038 2.00e-02 2.50e+03   1.60e-02 7.00e+00
        pdb=" N9   DA I  31 "    0.029 2.00e-02 2.50e+03
        pdb=" C8   DA I  31 "    0.014 2.00e-02 2.50e+03
        pdb=" N7   DA I  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I  31 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  31 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1   DA I  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DA I  31 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DA I  31 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 186
        2.63 -     3.20: 9662
        3.20 -     3.76: 21647
        3.76 -     4.33: 27367
        4.33 -     4.90: 38963
  Nonbonded interactions: 97825
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  69 "
            pdb=" NH1 ARG E  73 "
     model   vdw
     2.062 3.120
  nonbonded pdb=" N   ASN D  55 "
            pdb=" OP1  DA I  12 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG  SER C  41 "
            pdb=" OP1  DG J  98 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OH  TYR F  68 "
            pdb=" OE2 GLU H  75 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N2   DG I 114 "
            pdb=" O2   DT J  13 "
     model   vdw
     2.210 3.120
  ... (remaining 97820 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 51 through 140)
}
ncs_group {
  reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name  \ 
C ))))
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125))
  selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.250
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
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      :  0.009   0.083  11542  Z= 0.376
  Angle     :  0.883   7.680  16637  Z= 0.522
  Chirality :  0.054   0.237   1902
  Planarity :  0.005   0.042   1240
  Dihedral  : 28.860 153.423   4955
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  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: -1.18 (0.29), residues: 711
  helix: -0.22 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop : -2.04 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  64 
 TYR   0.020   0.003   TYR C  47 
 PHE   0.025   0.004   PHE C  94 
 HIS   0.016   0.002   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00886 (11542)
  covalent geometry    : angle       0.88264 (16637)
  hydrogen bonds       : bond        0.09313 (  707)
  hydrogen bonds       : angle       4.46578 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0)
REVERT: B   35 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7724 (mtt90)
REVERT: D   78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0)
REVERT: D   82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt)
REVERT: F   31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8033 (mmm160)
REVERT: F   87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt)
REVERT: H   51 LEU cc_start: 0.7360 (pp) cc_final: 0.7109 (pp)
REVERT: C   96 ASN cc_start: 0.8080 (p0) cc_final: 0.7802 (p0)
REVERT: C  101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10)
REVERT: G   85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1628
  time to fit residues: 25.6485
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 GLN
E  44 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.182377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.125845 restraints weight = 14853.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.127056 restraints weight = 9893.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.127569 restraints weight = 9538.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.128032 restraints weight = 8625.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.128121 restraints weight = 8526.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11542  Z= 0.173
  Angle     :  0.636   6.477  16637  Z= 0.374
  Chirality :  0.038   0.161   1902
  Planarity :  0.005   0.058   1240
  Dihedral  : 31.908 176.478   3513
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.40 %
    Favored  : 83.82 %
  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:  0.38 (0.29), residues: 711
  helix:  0.86 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.34 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 107 
 TYR   0.013   0.001   TYR E  55 
 PHE   0.020   0.002   PHE G  60 
 HIS   0.014   0.002   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11542)
  covalent geometry    : angle       0.63638 (16637)
  hydrogen bonds       : bond        0.04019 (  707)
  hydrogen bonds       : angle       3.45697 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7538 (mtt90)
REVERT: F   51 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7918 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8522 (ttmt)
REVERT: H   41 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: H   84 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7794 (mmtt)
REVERT: H   98 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8394 (ttmm)
REVERT: C  101 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: G   62 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7296 (mm-30)
  outliers start: 11
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1273
  time to fit residues: 20.0623
Evaluate side-chains
  98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 91 optimal weight:   20.0000
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
C  30 HIS
C  78 ASN
C  79 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.178875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.122484 restraints weight = 15103.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.122892 restraints weight = 11138.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.124022 restraints weight = 9970.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124483 restraints weight = 8620.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.124843 restraints weight = 8267.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11542  Z= 0.232
  Angle     :  0.646   7.597  16637  Z= 0.373
  Chirality :  0.039   0.172   1902
  Planarity :  0.005   0.046   1240
  Dihedral  : 31.780 176.249   3513
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.12 %
    Favored  : 78.64 %
  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:  0.67 (0.29), residues: 711
  helix:  1.10 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.32 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  39 
 TYR   0.014   0.002   TYR E  55 
 PHE   0.018   0.002   PHE G  60 
 HIS   0.010   0.002   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (11542)
  covalent geometry    : angle       0.64629 (16637)
  hydrogen bonds       : bond        0.04169 (  707)
  hydrogen bonds       : angle       3.39069 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: D   78 ASN cc_start: 0.8804 (t0) cc_final: 0.8228 (t0)
REVERT: D   82 ILE cc_start: 0.9084 (mt) cc_final: 0.8630 (mt)
REVERT: D  119 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8180 (tmmt)
REVERT: E   62 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7798 (mm)
REVERT: F   87 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8504 (ttmt)
REVERT: H   55 ASN cc_start: 0.8358 (t0) cc_final: 0.8118 (t0)
REVERT: H   84 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7761 (mmtt)
REVERT: H  104 GLU cc_start: 0.7607 (tp30) cc_final: 0.7386 (tp30)
REVERT: C   62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: C  101 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7817 (mt-10)
  outliers start: 20
  outliers final: 12
  residues processed: 119
  average time/residue: 0.1171
  time to fit residues: 19.0711
Evaluate side-chains
  105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.180100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.123860 restraints weight = 15131.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.124628 restraints weight = 10510.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125288 restraints weight = 9711.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.125872 restraints weight = 8771.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.126121 restraints weight = 8465.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11542  Z= 0.202
  Angle     :  0.619  13.017  16637  Z= 0.357
  Chirality :  0.037   0.154   1902
  Planarity :  0.005   0.067   1240
  Dihedral  : 31.540 177.274   3513
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.96 %
    Favored  : 78.64 %
  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:  0.95 (0.29), residues: 711
  helix:  1.33 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  36 
 TYR   0.013   0.002   TYR F  84 
 PHE   0.019   0.002   PHE G  60 
 HIS   0.010   0.002   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (11542)
  covalent geometry    : angle       0.61902 (16637)
  hydrogen bonds       : bond        0.03830 (  707)
  hydrogen bonds       : angle       3.27078 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.6998 (t0) cc_final: 0.6782 (t0)
REVERT: D  119 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8126 (tmmt)
REVERT: F   51 ARG cc_start: 0.8244 (mtt180) cc_final: 0.8028 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8550 (ttmt)
REVERT: H   55 ASN cc_start: 0.8268 (t0) cc_final: 0.7983 (t0)
REVERT: H   84 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7655 (mmtt)
REVERT: C   62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: C  101 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7740 (mt-10)
  outliers start: 21
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1171
  time to fit residues: 16.7309
Evaluate side-chains
  110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.181693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.125668 restraints weight = 15139.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126474 restraints weight = 10339.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.127015 restraints weight = 9602.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.127650 restraints weight = 8769.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127888 restraints weight = 8447.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11542  Z= 0.171
  Angle     :  0.586   9.630  16637  Z= 0.343
  Chirality :  0.036   0.139   1902
  Planarity :  0.004   0.045   1240
  Dihedral  : 31.330 177.324   3513
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.26 %
    Favored  : 77.51 %
  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:  1.43 (0.30), residues: 711
  helix:  1.72 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.20 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  39 
 TYR   0.010   0.001   TYR E 102 
 PHE   0.015   0.002   PHE G  60 
 HIS   0.008   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11542)
  covalent geometry    : angle       0.58615 (16637)
  hydrogen bonds       : bond        0.03647 (  707)
  hydrogen bonds       : angle       3.16260 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.290 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7543 (m-40) cc_final: 0.7126 (m-40)
REVERT: F   51 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7971 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8529 (ttmt)
REVERT: H   55 ASN cc_start: 0.8354 (t0) cc_final: 0.8036 (t0)
REVERT: H   84 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7699 (mmtt)
REVERT: H  104 GLU cc_start: 0.7562 (tp30) cc_final: 0.7048 (tp30)
REVERT: H  107 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7611 (ttp80)
REVERT: C   62 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7424 (mm-30)
REVERT: C   73 LYS cc_start: 0.7152 (tttm) cc_final: 0.6945 (tttm)
REVERT: C  101 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7719 (mt-10)
  outliers start: 20
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1304
  time to fit residues: 19.7961
Evaluate side-chains
  108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
E  44 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.127005 restraints weight = 15144.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.129112 restraints weight = 9963.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.129352 restraints weight = 8916.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.129696 restraints weight = 8320.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130187 restraints weight = 7562.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11542  Z= 0.159
  Angle     :  0.576   9.165  16637  Z= 0.337
  Chirality :  0.035   0.145   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.135 178.659   3513
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.87 %
    Favored  : 76.70 %
  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:  1.71 (0.30), residues: 711
  helix:  1.94 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.15 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  36 
 TYR   0.010   0.001   TYR F  84 
 PHE   0.015   0.002   PHE G  60 
 HIS   0.008   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11542)
  covalent geometry    : angle       0.57633 (16637)
  hydrogen bonds       : bond        0.03578 (  707)
  hydrogen bonds       : angle       3.10572 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLU cc_start: 0.8032 (tp30) cc_final: 0.7712 (tp30)
REVERT: D   86 ASN cc_start: 0.7625 (m-40) cc_final: 0.7230 (m-40)
REVERT: D  108 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8361 (mp)
REVERT: F   51 ARG cc_start: 0.8217 (mtt180) cc_final: 0.8006 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8518 (ttmt)
REVERT: H   55 ASN cc_start: 0.8314 (t0) cc_final: 0.7978 (t0)
REVERT: H  104 GLU cc_start: 0.7599 (tp30) cc_final: 0.7249 (tp30)
REVERT: H  107 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7692 (ttp80)
REVERT: C   62 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7437 (mm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1326
  time to fit residues: 18.9875
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 61 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.181943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.126104 restraints weight = 15212.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.127087 restraints weight = 10212.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.127650 restraints weight = 9339.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128293 restraints weight = 8481.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128521 restraints weight = 8142.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11542  Z= 0.176
  Angle     :  0.579  11.040  16637  Z= 0.337
  Chirality :  0.035   0.138   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 31.061 178.510   3513
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.74 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.29), residues: 711
  helix:  1.90 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.14 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  36 
 TYR   0.021   0.002   TYR F  84 
 PHE   0.015   0.002   PHE G  60 
 HIS   0.006   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (11542)
  covalent geometry    : angle       0.57905 (16637)
  hydrogen bonds       : bond        0.03669 (  707)
  hydrogen bonds       : angle       3.13975 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8065 (tp30) cc_final: 0.7681 (tp30)
REVERT: D   43 ILE cc_start: 0.6633 (mm) cc_final: 0.6388 (mt)
REVERT: D   86 ASN cc_start: 0.7644 (m-40) cc_final: 0.7224 (m-40)
REVERT: D  108 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8426 (mp)
REVERT: D  119 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8226 (tttp)
REVERT: F   51 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7960 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8538 (ttmt)
REVERT: H   55 ASN cc_start: 0.8312 (t0) cc_final: 0.7978 (t0)
REVERT: H  104 GLU cc_start: 0.7650 (tp30) cc_final: 0.7303 (tp30)
REVERT: H  107 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7671 (ttp80)
  outliers start: 24
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1238
  time to fit residues: 18.3916
Evaluate side-chains
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0980
   chunk 49 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.183224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127466 restraints weight = 15162.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.127988 restraints weight = 10364.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128735 restraints weight = 9620.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.129286 restraints weight = 8697.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.129521 restraints weight = 8437.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11542  Z= 0.161
  Angle     :  0.567   9.989  16637  Z= 0.333
  Chirality :  0.035   0.132   1902
  Planarity :  0.004   0.042   1240
  Dihedral  : 30.931 178.874   3513
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.06 %
    Favored  : 76.86 %
  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:  1.82 (0.30), residues: 711
  helix:  2.01 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.06 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  36 
 TYR   0.012   0.001   TYR F  84 
 PHE   0.024   0.002   PHE C  94 
 HIS   0.006   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11542)
  covalent geometry    : angle       0.56720 (16637)
  hydrogen bonds       : bond        0.03574 (  707)
  hydrogen bonds       : angle       3.10651 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.277 
Fit side-chains
REVERT: D   43 ILE cc_start: 0.6646 (mm) cc_final: 0.6439 (mt)
REVERT: D   86 ASN cc_start: 0.7641 (m-40) cc_final: 0.7238 (m-40)
REVERT: D  108 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8447 (mp)
REVERT: D  119 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8222 (tttp)
REVERT: H   55 ASN cc_start: 0.8325 (t0) cc_final: 0.8016 (t0)
REVERT: H   85 ARG cc_start: 0.8165 (ptt90) cc_final: 0.7928 (ptt90)
  outliers start: 19
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1209
  time to fit residues: 16.7735
Evaluate side-chains
  104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.180441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.122616 restraints weight = 14928.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.123995 restraints weight = 10518.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124255 restraints weight = 9337.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124991 restraints weight = 8597.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125492 restraints weight = 7845.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11542  Z= 0.159
  Angle     :  0.564   9.399  16637  Z= 0.331
  Chirality :  0.035   0.142   1902
  Planarity :  0.004   0.042   1240
  Dihedral  : 30.834 178.640   3513
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.23 %
    Favored  : 76.54 %
  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:  1.86 (0.30), residues: 711
  helix:  2.03 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.01 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  36 
 TYR   0.017   0.002   TYR F  84 
 PHE   0.015   0.002   PHE C  94 
 HIS   0.006   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (11542)
  covalent geometry    : angle       0.56423 (16637)
  hydrogen bonds       : bond        0.03592 (  707)
  hydrogen bonds       : angle       3.08791 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.333 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7717 (m-40) cc_final: 0.7336 (m-40)
REVERT: D  108 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8461 (mp)
REVERT: H   55 ASN cc_start: 0.8361 (t0) cc_final: 0.7978 (t0)
REVERT: H   85 ARG cc_start: 0.7992 (ptt90) cc_final: 0.7749 (ptt90)
  outliers start: 20
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1231
  time to fit residues: 16.6361
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.180201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.122257 restraints weight = 14983.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123769 restraints weight = 10508.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.123939 restraints weight = 9395.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.124459 restraints weight = 8674.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.125047 restraints weight = 7899.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  11542  Z= 0.223
  Angle     :  0.814  59.199  16637  Z= 0.492
  Chirality :  0.036   0.462   1902
  Planarity :  0.005   0.070   1240
  Dihedral  : 30.836 178.650   3513
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.09 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.04 %
    Favored  : 76.21 %
  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:  1.85 (0.30), residues: 711
  helix:  2.02 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  51 
 TYR   0.015   0.001   TYR F  84 
 PHE   0.014   0.002   PHE C  94 
 HIS   0.006   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (11542)
  covalent geometry    : angle       0.81384 (16637)
  hydrogen bonds       : bond        0.03595 (  707)
  hydrogen bonds       : angle       3.08382 ( 1794)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.267 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7715 (m-40) cc_final: 0.7330 (m-40)
REVERT: D  108 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8463 (mp)
REVERT: H   55 ASN cc_start: 0.8352 (t0) cc_final: 0.7973 (t0)
REVERT: H   85 ARG cc_start: 0.8017 (ptt90) cc_final: 0.7745 (ptt90)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1094
  time to fit residues: 14.5581
Evaluate side-chains
  97 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.180190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.122484 restraints weight = 15064.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123880 restraints weight = 10383.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124028 restraints weight = 9522.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.124700 restraints weight = 8680.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.124895 restraints weight = 8485.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  11542  Z= 0.223
  Angle     :  0.814  59.199  16637  Z= 0.492
  Chirality :  0.036   0.462   1902
  Planarity :  0.005   0.070   1240
  Dihedral  : 30.836 178.650   3513
  Min Nonbonded Distance : 1.520

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.09 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.04 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.30), residues: 711
  helix:  2.02 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  51 
 TYR   0.015   0.001   TYR F  84 
 PHE   0.014   0.002   PHE C  94 
 HIS   0.006   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (11542)
  covalent geometry    : angle       0.81384 (16637)
  hydrogen bonds       : bond        0.03595 (  707)
  hydrogen bonds       : angle       3.08382 ( 1794)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1390.77 seconds
wall clock time: 24 minutes 49.41 seconds (1489.41 seconds total)