Starting phenix.real_space_refine
on Wed Mar  4 02:42:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dbh_30631/03_2026/7dbh_30631.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.004
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      14      5.16       5
     C    5902      2.51       5
     N    1973      2.21       5
     O    2492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  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: 10631
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 612
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 2, 'TRANS': 75}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 677
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "F"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 614
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 740
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "I"
      Number of atoms: 2563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2563
          Classifications: {'DNA': 126}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 125}
    Chain: "J"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2597
          Classifications: {'DNA': 126}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 125}
  Time building chain proxies: 2.27, per 1000 atoms: 0.21
  Number of scatterers: 10631
  At special positions: 0
  Unit cell: (122.1, 75.9, 115.5, 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      14     16.00
     P     250     15.00
     O    2492      8.00
     N    1973      7.00
     C    5902      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: 0.74
  Conformation dependent library (CDL) restraints added in 338.6 milliseconds
  

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      76.8% alpha, 2.9% beta
      116 base pairs and 191 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.717A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.608A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 18 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.314A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'E' and resid 49 through 57
      removed outlier: 3.638A  pdb=" N   SER E  57 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 47 through 76
      removed outlier: 4.151A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.383A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 98
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.824A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.777A  pdb=" N   CYS A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.821A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.864A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.435A  pdb=" N   CYS E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.257A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    403 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      303 hydrogen bonds
      594 hydrogen bond angles
      0 basepair planarities
      116 basepair parallelities
      191 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 1.00 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: 2284
        1.33 -     1.45: 3447
        1.45 -     1.57: 5077
        1.57 -     1.69: 500
        1.69 -     1.81: 22
  Bond restraints: 11330
  Sorted by residual:
  bond pdb=" N   ILE E 130 "
       pdb=" CA  ILE E 130 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.14e-02 7.69e+03 8.54e+00
  bond pdb=" N   ARG A  63 "
       pdb=" CA  ARG A  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.23e-02 6.61e+03 7.54e+00
  bond pdb=" N   ARG G  42 "
       pdb=" CA  ARG G  42 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.031 1.23e-02 6.61e+03 6.18e+00
  bond pdb=" N   GLY H  32 "
       pdb=" CA  GLY H  32 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.17e+00
  bond pdb=" N   CYS E 131 "
       pdb=" CA  CYS E 131 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.03e+00
  ... (remaining 11325 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 14978
        1.25 -     2.50: 1181
        2.50 -     3.75: 211
        3.75 -     5.00: 11
        5.00 -     6.25: 4
  Bond angle restraints: 16385
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.71  109.21    4.50 9.50e-01 1.11e+00 2.25e+01
  angle pdb=" O   CYS E 131 "
        pdb=" C   CYS E 131 "
        pdb=" N   ARG E 132 "
      ideal   model   delta    sigma   weight residual
     122.12  125.71   -3.59 1.06e+00 8.90e-01 1.15e+01
  angle pdb=" C   ARG A 132 "
        pdb=" CA  ARG A 132 "
        pdb=" CB  ARG A 132 "
      ideal   model   delta    sigma   weight residual
     110.10  116.35   -6.25 1.90e+00 2.77e-01 1.08e+01
  angle pdb=" N   ARG C  17 "
        pdb=" CA  ARG C  17 "
        pdb=" C   ARG C  17 "
      ideal   model   delta    sigma   weight residual
     113.43  109.44    3.99 1.26e+00 6.30e-01 1.00e+01
  angle pdb=" N   ARG B  55 "
        pdb=" CA  ARG B  55 "
        pdb=" C   ARG B  55 "
      ideal   model   delta    sigma   weight residual
     111.28  107.92    3.36 1.09e+00 8.42e-01 9.51e+00
  ... (remaining 16380 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.66: 4874
       33.66 -    67.32: 1205
       67.32 -   100.98: 41
      100.98 -   134.65: 5
      134.65 -   168.31: 5
  Dihedral angle restraints: 6130
    sinusoidal: 4116
      harmonic: 2014
  Sorted by residual:
  dihedral pdb=" C   ARG A 132 "
           pdb=" N   ARG A 132 "
           pdb=" CA  ARG A 132 "
           pdb=" CB  ARG A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.04   10.44     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.69  168.31     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DC J -58 "
           pdb=" C3'  DC J -58 "
           pdb=" O3'  DC J -58 "
           pdb=" P    DT J -57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.95  168.05     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 6127 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1510
       0.060 -    0.120: 349
       0.120 -    0.180: 14
       0.180 -    0.241: 0
       0.241 -    0.301: 1
  Chirality restraints: 1874
  Sorted by residual:
  chirality pdb=" CA  ARG A 132 "
            pdb=" N   ARG A 132 "
            pdb=" C   ARG A 132 "
            pdb=" CB  ARG A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  LEU E 100 "
            pdb=" N   LEU E 100 "
            pdb=" C   LEU E 100 "
            pdb=" CB  LEU E 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CA  LEU F  37 "
            pdb=" N   LEU F  37 "
            pdb=" C   LEU F  37 "
            pdb=" CB  LEU F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.91e-01
  ... (remaining 1871 not shown)

  Planarity restraints: 1197
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -36 "    0.016 2.00e-02 2.50e+03   1.08e-02 3.50e+00
        pdb=" N9   DG J -36 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DG J -36 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG J -36 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J -36 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J -36 "   -0.021 2.00e-02 2.50e+03
        pdb=" O6   DG J -36 "    0.015 2.00e-02 2.50e+03
        pdb=" N1   DG J -36 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG J -36 "    0.008 2.00e-02 2.50e+03
        pdb=" N2   DG J -36 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG J -36 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG J -36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  35 "   -0.007 2.00e-02 2.50e+03   1.20e-02 3.22e+00
        pdb=" N1   DC I  35 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DC I  35 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DC I  35 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DC I  35 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DC I  35 "    0.028 2.00e-02 2.50e+03
        pdb=" N4   DC I  35 "   -0.017 2.00e-02 2.50e+03
        pdb=" C5   DC I  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I  35 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   6 "   -0.022 2.00e-02 2.50e+03   1.16e-02 3.05e+00
        pdb=" N1   DC I   6 "    0.023 2.00e-02 2.50e+03
        pdb=" C2   DC I   6 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DC I   6 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   6 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC I   6 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC I   6 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I   6 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC I   6 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1194 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 1
        2.14 -     2.83: 3202
        2.83 -     3.52: 18486
        3.52 -     4.21: 29919
        4.21 -     4.90: 44435
  Nonbonded interactions: 96043
  Sorted by model distance:
  nonbonded pdb=" O   ALA F  33 "
            pdb=" CD2 LEU F  37 "
     model   vdw
     1.451 3.460
  nonbonded pdb=" O   HIS H 109 "
            pdb=" OG  SER H 112 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" N2   DG I  58 "
            pdb=" O2   DT J -57 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" N2   DG I -60 "
            pdb=" O2   DC J  61 "
     model   vdw
     2.206 3.120
  ... (remaining 96038 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 55 through 132)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 109)
}
ncs_group {
  reference = (chain 'D' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ 
e C or name CB or name OG ))))
  selection = (chain 'H' and resid 33 through 124)
}

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:             0.560
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.080
  Find NCS groups from input model:        0.250
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
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      :  0.007   0.042  11330  Z= 0.366
  Angle     :  0.740   6.252  16385  Z= 0.488
  Chirality :  0.047   0.301   1874
  Planarity :  0.003   0.019   1197
  Dihedral  : 28.574 168.307   4834
  Min Nonbonded Distance : 1.451

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.17 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.15 %
  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:  0.54 (0.31), residues: 681
  helix:  1.01 (0.22), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.62 (0.42), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  39 
 TYR   0.017   0.002   TYR D  83 
 PHE   0.009   0.002   PHE C  25 
 HIS   0.011   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 (11330)
  covalent geometry    : angle       0.74032 (16385)
  hydrogen bonds       : bond        0.11044 (  706)
  hydrogen bonds       : angle       5.01185 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PRO C 109 " (corrupted residue). Skipping it.
Corrupt residue: chain: C residue: PRO 109 >>> skipping
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9292 (mt0) cc_final: 0.9057 (mt0)
REVERT: A   97 GLU cc_start: 0.8443 (tt0) cc_final: 0.8192 (tt0)
REVERT: A  120 MET cc_start: 0.8495 (mtp) cc_final: 0.8029 (mtp)
REVERT: A  124 THR cc_start: 0.9775 (m) cc_final: 0.9562 (p)
REVERT: B   44 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8685 (mmmt)
REVERT: B   79 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8831 (mtmm)
REVERT: B   80 THR cc_start: 0.9530 (m) cc_final: 0.9200 (p)
REVERT: B   85 ASP cc_start: 0.8843 (m-30) cc_final: 0.8590 (m-30)
REVERT: C   64 GLU cc_start: 0.8535 (tp30) cc_final: 0.8137 (tp30)
REVERT: C  104 GLN cc_start: 0.8689 (mp10) cc_final: 0.7987 (mp10)
REVERT: D   68 ASP cc_start: 0.9159 (t70) cc_final: 0.8695 (t0)
REVERT: D   71 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8782 (tm-30)
REVERT: D   85 LYS cc_start: 0.9504 (mttm) cc_final: 0.9271 (mtmm)
REVERT: E   80 THR cc_start: 0.8924 (p) cc_final: 0.8681 (p)
REVERT: E   82 LEU cc_start: 0.9401 (mt) cc_final: 0.9021 (mt)
REVERT: E  120 MET cc_start: 0.8432 (mtp) cc_final: 0.8219 (mtp)
REVERT: F   39 ARG cc_start: 0.9363 (mmt90) cc_final: 0.9163 (tpp-160)
REVERT: F   50 ILE cc_start: 0.9608 (mm) cc_final: 0.9354 (mm)
REVERT: F   52 GLU cc_start: 0.8730 (tp30) cc_final: 0.8451 (tm-30)
REVERT: G   39 TYR cc_start: 0.9215 (m-80) cc_final: 0.8933 (m-80)
REVERT: G   56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8651 (tt0)
REVERT: G   57 TYR cc_start: 0.8993 (t80) cc_final: 0.8687 (t80)
REVERT: G   64 GLU cc_start: 0.8730 (tp30) cc_final: 0.8268 (tp30)
REVERT: H   46 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9215 (mmmt)
REVERT: H   71 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: H  113 GLU cc_start: 0.9257 (tp30) cc_final: 0.8775 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1253
  time to fit residues: 34.6663
Evaluate side-chains
  156 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
D  49 HIS
E 125 GLN
H 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.062940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.041120 restraints weight = 54098.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.042309 restraints weight = 28105.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.043053 restraints weight = 20139.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.043477 restraints weight = 17039.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.043575 restraints weight = 15641.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11330  Z= 0.177
  Angle     :  0.645   5.833  16385  Z= 0.379
  Chirality :  0.037   0.163   1874
  Planarity :  0.004   0.035   1197
  Dihedral  : 32.055 178.922   3499
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.40 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.31), residues: 681
  helix:  2.49 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.21 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  63 
 TYR   0.038   0.002   TYR D  83 
 PHE   0.015   0.002   PHE A  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (11330)
  covalent geometry    : angle       0.64518 (16385)
  hydrogen bonds       : bond        0.04579 (  706)
  hydrogen bonds       : angle       3.44236 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 222
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9271 (mt0) cc_final: 0.8753 (mt0)
REVERT: A   97 GLU cc_start: 0.8461 (tt0) cc_final: 0.8231 (tt0)
REVERT: A  107 THR cc_start: 0.9579 (m) cc_final: 0.9361 (p)
REVERT: A  125 GLN cc_start: 0.9205 (mt0) cc_final: 0.8409 (mp10)
REVERT: B   44 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8696 (mmmt)
REVERT: B   96 THR cc_start: 0.9440 (m) cc_final: 0.9123 (p)
REVERT: C   24 GLN cc_start: 0.9321 (mm110) cc_final: 0.8910 (mp10)
REVERT: C   38 ASN cc_start: 0.8404 (t0) cc_final: 0.7959 (t0)
REVERT: C   56 GLU cc_start: 0.8504 (tt0) cc_final: 0.8246 (tt0)
REVERT: C   64 GLU cc_start: 0.8659 (tp30) cc_final: 0.8341 (tp30)
REVERT: C  104 GLN cc_start: 0.8401 (mp10) cc_final: 0.7878 (mp10)
REVERT: D   46 LYS cc_start: 0.9582 (mmtp) cc_final: 0.9269 (mmtp)
REVERT: D   68 ASP cc_start: 0.9018 (t0) cc_final: 0.8784 (t70)
REVERT: D   71 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8656 (tm-30)
REVERT: D  113 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8553 (mt-10)
REVERT: D  120 LYS cc_start: 0.9522 (ttpt) cc_final: 0.9169 (ttpp)
REVERT: E   80 THR cc_start: 0.8939 (p) cc_final: 0.8728 (t)
REVERT: E  125 GLN cc_start: 0.8367 (tm130) cc_final: 0.8061 (tm-30)
REVERT: F   52 GLU cc_start: 0.8589 (tp30) cc_final: 0.8354 (tm-30)
REVERT: F   63 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8418 (mt-10)
REVERT: F   73 THR cc_start: 0.9636 (m) cc_final: 0.9414 (p)
REVERT: F   85 ASP cc_start: 0.8860 (m-30) cc_final: 0.8555 (m-30)
REVERT: G   57 TYR cc_start: 0.8967 (t80) cc_final: 0.8448 (t80)
REVERT: G   64 GLU cc_start: 0.8733 (tp30) cc_final: 0.8148 (tp30)
REVERT: G   84 GLN cc_start: 0.9429 (tp-100) cc_final: 0.8978 (tp-100)
REVERT: H   46 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9183 (mmmt)
REVERT: H   71 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8631 (tm-30)
REVERT: H   93 GLU cc_start: 0.8633 (mp0) cc_final: 0.8230 (mp0)
REVERT: H  113 GLU cc_start: 0.9170 (tp30) cc_final: 0.8741 (tt0)
  outliers start: 12
  outliers final: 5
  residues processed: 226
  average time/residue: 0.1025
  time to fit residues: 32.4527
Evaluate side-chains
  183 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 178
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.062477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.040168 restraints weight = 55075.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.041243 restraints weight = 29847.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.041903 restraints weight = 21893.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.042312 restraints weight = 18782.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.042416 restraints weight = 17349.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11330  Z= 0.188
  Angle     :  0.612   7.720  16385  Z= 0.359
  Chirality :  0.035   0.153   1874
  Planarity :  0.004   0.036   1197
  Dihedral  : 31.765 177.823   3499
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.83 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.31), residues: 681
  helix:  2.54 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.93 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  92 
 TYR   0.040   0.002   TYR D  83 
 PHE   0.013   0.002   PHE A  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11330)
  covalent geometry    : angle       0.61183 (16385)
  hydrogen bonds       : bond        0.04469 (  706)
  hydrogen bonds       : angle       3.31887 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9121 (mt0) cc_final: 0.8693 (mt0)
REVERT: A   97 GLU cc_start: 0.8466 (tt0) cc_final: 0.8230 (tt0)
REVERT: A  125 GLN cc_start: 0.9168 (mt0) cc_final: 0.8366 (mp10)
REVERT: C   24 GLN cc_start: 0.9293 (mm110) cc_final: 0.8959 (mp10)
REVERT: C   38 ASN cc_start: 0.8314 (t0) cc_final: 0.7844 (t0)
REVERT: C   56 GLU cc_start: 0.8584 (tt0) cc_final: 0.8264 (tt0)
REVERT: C   64 GLU cc_start: 0.8588 (tp30) cc_final: 0.8348 (tp30)
REVERT: C  104 GLN cc_start: 0.8506 (mp10) cc_final: 0.7915 (mp10)
REVERT: D   46 LYS cc_start: 0.9563 (mmtp) cc_final: 0.9170 (mmtt)
REVERT: D   68 ASP cc_start: 0.9092 (t70) cc_final: 0.8818 (t70)
REVERT: D   71 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: D  120 LYS cc_start: 0.9473 (ttpt) cc_final: 0.9141 (ttpp)
REVERT: E  123 ASP cc_start: 0.8838 (m-30) cc_final: 0.8365 (m-30)
REVERT: E  125 GLN cc_start: 0.8433 (tm130) cc_final: 0.8090 (tm-30)
REVERT: F   39 ARG cc_start: 0.9173 (tpp-160) cc_final: 0.8595 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8585 (tp30) cc_final: 0.8274 (tm-30)
REVERT: F   63 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8388 (mt-10)
REVERT: F   73 THR cc_start: 0.9620 (m) cc_final: 0.9346 (p)
REVERT: G   39 TYR cc_start: 0.9297 (m-80) cc_final: 0.9073 (m-80)
REVERT: G   57 TYR cc_start: 0.9034 (t80) cc_final: 0.8513 (t80)
REVERT: G   64 GLU cc_start: 0.8648 (tp30) cc_final: 0.7877 (tp30)
REVERT: G   84 GLN cc_start: 0.9409 (tp-100) cc_final: 0.8938 (tp-100)
REVERT: G   89 ASN cc_start: 0.9389 (m-40) cc_final: 0.9049 (m110)
REVERT: G   90 ASP cc_start: 0.8316 (t0) cc_final: 0.8017 (t0)
REVERT: G   92 GLU cc_start: 0.9006 (mp0) cc_final: 0.8603 (pm20)
REVERT: H   46 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9176 (mmmt)
REVERT: H   71 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8607 (tm-30)
REVERT: H   93 GLU cc_start: 0.8615 (mp0) cc_final: 0.8146 (mp0)
REVERT: H  113 GLU cc_start: 0.9116 (tp30) cc_final: 0.8700 (tt0)
  outliers start: 20
  outliers final: 12
  residues processed: 208
  average time/residue: 0.0941
  time to fit residues: 27.8562
Evaluate side-chains
  194 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0370
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.9664

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.062004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.039521 restraints weight = 55559.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.040598 restraints weight = 30095.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.041279 restraints weight = 22143.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041679 restraints weight = 18984.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.041858 restraints weight = 17559.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11330  Z= 0.204
  Angle     :  0.609   6.974  16385  Z= 0.357
  Chirality :  0.035   0.154   1874
  Planarity :  0.004   0.036   1197
  Dihedral  : 31.672 177.018   3499
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.83 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.31), residues: 681
  helix:  2.60 (0.21), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.67 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  92 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (11330)
  covalent geometry    : angle       0.60902 (16385)
  hydrogen bonds       : bond        0.04482 (  706)
  hydrogen bonds       : angle       3.22218 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9116 (mt0) cc_final: 0.8718 (mt0)
REVERT: A   97 GLU cc_start: 0.8422 (tt0) cc_final: 0.7977 (tt0)
REVERT: A  125 GLN cc_start: 0.9210 (mt0) cc_final: 0.8334 (mp10)
REVERT: B   44 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8859 (tppt)
REVERT: C   24 GLN cc_start: 0.9322 (mm110) cc_final: 0.9004 (mp10)
REVERT: C   38 ASN cc_start: 0.8287 (t0) cc_final: 0.7893 (t0)
REVERT: C   73 ASN cc_start: 0.8973 (t0) cc_final: 0.8614 (t0)
REVERT: C  104 GLN cc_start: 0.8545 (mp10) cc_final: 0.7989 (mp10)
REVERT: D   46 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9227 (mmmt)
REVERT: D   68 ASP cc_start: 0.9080 (t70) cc_final: 0.8767 (t70)
REVERT: D   71 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: D  120 LYS cc_start: 0.9504 (ttpt) cc_final: 0.9136 (ttpp)
REVERT: E   79 LYS cc_start: 0.8630 (tmtt) cc_final: 0.7926 (tmtt)
REVERT: E  123 ASP cc_start: 0.8806 (m-30) cc_final: 0.8314 (m-30)
REVERT: E  125 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: F   39 ARG cc_start: 0.9194 (tpp-160) cc_final: 0.8595 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8641 (tp30) cc_final: 0.8269 (tm-30)
REVERT: F   63 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8335 (mt-10)
REVERT: F   73 THR cc_start: 0.9611 (m) cc_final: 0.9295 (p)
REVERT: G   57 TYR cc_start: 0.9058 (t80) cc_final: 0.8517 (t80)
REVERT: G   64 GLU cc_start: 0.8580 (tp30) cc_final: 0.7950 (tp30)
REVERT: G   84 GLN cc_start: 0.9383 (tp-100) cc_final: 0.9091 (tp-100)
REVERT: G   89 ASN cc_start: 0.9388 (m-40) cc_final: 0.8996 (m110)
REVERT: G   90 ASP cc_start: 0.8404 (t0) cc_final: 0.7928 (t0)
REVERT: G   92 GLU cc_start: 0.8984 (mp0) cc_final: 0.8486 (pm20)
REVERT: H   46 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9178 (mmmt)
REVERT: H   71 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: H  113 GLU cc_start: 0.9123 (tp30) cc_final: 0.8701 (tt0)
  outliers start: 22
  outliers final: 17
  residues processed: 195
  average time/residue: 0.0989
  time to fit residues: 27.2490
Evaluate side-chains
  195 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   overall best weight:    5.9994

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.060405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037562 restraints weight = 55307.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.038609 restraints weight = 30555.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.039270 restraints weight = 22651.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.039640 restraints weight = 19472.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.039734 restraints weight = 18079.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  11330  Z= 0.317
  Angle     :  0.672   7.834  16385  Z= 0.388
  Chirality :  0.038   0.183   1874
  Planarity :  0.004   0.040   1197
  Dihedral  : 31.888 179.388   3499
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 19.34 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.31), residues: 681
  helix:  2.42 (0.21), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.79 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  92 
 TYR   0.011   0.002   TYR E  54 
 PHE   0.016   0.002   PHE A  67 
 HIS   0.005   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00705 (11330)
  covalent geometry    : angle       0.67228 (16385)
  hydrogen bonds       : bond        0.05685 (  706)
  hydrogen bonds       : angle       3.45343 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9193 (mt0) cc_final: 0.8708 (mt0)
REVERT: B   50 ILE cc_start: 0.9540 (tp) cc_final: 0.9285 (mm)
REVERT: B   88 TYR cc_start: 0.9132 (m-10) cc_final: 0.8851 (m-80)
REVERT: C   24 GLN cc_start: 0.9382 (mm110) cc_final: 0.9121 (mp10)
REVERT: C   38 ASN cc_start: 0.8426 (t0) cc_final: 0.8045 (t0)
REVERT: C   73 ASN cc_start: 0.9039 (t0) cc_final: 0.8681 (t0)
REVERT: C  104 GLN cc_start: 0.8666 (mp10) cc_final: 0.8073 (mp10)
REVERT: D   46 LYS cc_start: 0.9523 (mmtp) cc_final: 0.9178 (mmmt)
REVERT: D   68 ASP cc_start: 0.9094 (t70) cc_final: 0.8629 (t0)
REVERT: D   71 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8576 (tm-30)
REVERT: D  120 LYS cc_start: 0.9559 (ttpt) cc_final: 0.9171 (ttpp)
REVERT: E   79 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8126 (tmtt)
REVERT: E  123 ASP cc_start: 0.8829 (m-30) cc_final: 0.8399 (m-30)
REVERT: E  125 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: F   39 ARG cc_start: 0.9204 (tpp-160) cc_final: 0.8767 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8706 (tp30) cc_final: 0.8340 (tm-30)
REVERT: F   63 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8571 (mt-10)
REVERT: F   73 THR cc_start: 0.9637 (m) cc_final: 0.9320 (p)
REVERT: F   85 ASP cc_start: 0.8738 (m-30) cc_final: 0.8379 (m-30)
REVERT: G   38 ASN cc_start: 0.9128 (m-40) cc_final: 0.8736 (m-40)
REVERT: G   57 TYR cc_start: 0.9083 (t80) cc_final: 0.8788 (t80)
REVERT: G   64 GLU cc_start: 0.8533 (tp30) cc_final: 0.7913 (tp30)
REVERT: G   89 ASN cc_start: 0.9408 (m-40) cc_final: 0.9006 (m110)
REVERT: G   90 ASP cc_start: 0.8610 (t0) cc_final: 0.8020 (t0)
REVERT: G   92 GLU cc_start: 0.9050 (mp0) cc_final: 0.8472 (pm20)
REVERT: H   46 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9224 (mmmt)
REVERT: H   93 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8294 (mm-30)
  outliers start: 26
  outliers final: 21
  residues processed: 186
  average time/residue: 0.0978
  time to fit residues: 25.8491
Evaluate side-chains
  185 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.063021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.040273 restraints weight = 54260.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.041358 restraints weight = 28970.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.042073 restraints weight = 21264.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.042421 restraints weight = 18189.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.042632 restraints weight = 16925.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11330  Z= 0.166
  Angle     :  0.613   7.622  16385  Z= 0.357
  Chirality :  0.035   0.162   1874
  Planarity :  0.004   0.043   1197
  Dihedral  : 31.579 178.296   3499
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.97 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.31), residues: 681
  helix:  2.51 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.68 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  63 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.019   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11330)
  covalent geometry    : angle       0.61272 (16385)
  hydrogen bonds       : bond        0.04188 (  706)
  hydrogen bonds       : angle       3.10891 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9113 (mt0) cc_final: 0.8644 (mt0)
REVERT: B   88 TYR cc_start: 0.9067 (m-10) cc_final: 0.8860 (m-80)
REVERT: C   73 ASN cc_start: 0.8984 (t0) cc_final: 0.8523 (t0)
REVERT: C  104 GLN cc_start: 0.8584 (mp10) cc_final: 0.7982 (mp10)
REVERT: D   46 LYS cc_start: 0.9460 (mmtp) cc_final: 0.9190 (mmmt)
REVERT: D   68 ASP cc_start: 0.9090 (t70) cc_final: 0.8830 (t70)
REVERT: D   71 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8575 (tm-30)
REVERT: D  120 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9122 (ttpp)
REVERT: E   79 LYS cc_start: 0.8645 (tmtt) cc_final: 0.7983 (tmtt)
REVERT: E   93 GLN cc_start: 0.8847 (tp40) cc_final: 0.8399 (tp40)
REVERT: E  125 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8373 (tm-30)
REVERT: F   39 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8600 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8577 (tp30) cc_final: 0.8206 (tm-30)
REVERT: F   63 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: F   73 THR cc_start: 0.9623 (m) cc_final: 0.9349 (p)
REVERT: F   88 TYR cc_start: 0.9146 (m-10) cc_final: 0.8923 (m-10)
REVERT: G   59 THR cc_start: 0.9667 (m) cc_final: 0.9295 (t)
REVERT: G   84 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9157 (tp-100)
REVERT: G   89 ASN cc_start: 0.9394 (m-40) cc_final: 0.8994 (m110)
REVERT: G   90 ASP cc_start: 0.8435 (t0) cc_final: 0.7875 (t0)
REVERT: G   92 GLU cc_start: 0.9007 (mp0) cc_final: 0.8476 (pm20)
REVERT: H   46 LYS cc_start: 0.9434 (mmmt) cc_final: 0.9143 (mmmt)
REVERT: H   93 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8141 (mm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 197
  average time/residue: 0.0962
  time to fit residues: 26.9638
Evaluate side-chains
  189 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 31 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.063484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.041385 restraints weight = 52559.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.042528 restraints weight = 27567.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.043243 restraints weight = 19816.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.043641 restraints weight = 16777.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.043740 restraints weight = 15425.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11330  Z= 0.165
  Angle     :  0.613   8.697  16385  Z= 0.356
  Chirality :  0.035   0.179   1874
  Planarity :  0.004   0.045   1197
  Dihedral  : 31.391 177.263   3499
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 25.22 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.31), residues: 681
  helix:  2.64 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.60 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  92 
 TYR   0.022   0.002   TYR C  57 
 PHE   0.012   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (11330)
  covalent geometry    : angle       0.61321 (16385)
  hydrogen bonds       : bond        0.04071 (  706)
  hydrogen bonds       : angle       3.01686 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 193
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9030 (mt0) cc_final: 0.8733 (mt0)
REVERT: C   73 ASN cc_start: 0.8924 (t0) cc_final: 0.8452 (t0)
REVERT: C  104 GLN cc_start: 0.8588 (mp10) cc_final: 0.7839 (mp10)
REVERT: D   46 LYS cc_start: 0.9478 (mmtp) cc_final: 0.9121 (mmmt)
REVERT: D   68 ASP cc_start: 0.9077 (t70) cc_final: 0.8838 (t70)
REVERT: D   71 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: D  120 LYS cc_start: 0.9450 (ttpt) cc_final: 0.9088 (ttpp)
REVERT: E   79 LYS cc_start: 0.8657 (tmtt) cc_final: 0.7920 (tmtt)
REVERT: E  105 GLU cc_start: 0.8658 (tt0) cc_final: 0.8366 (tp30)
REVERT: E  125 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: F   39 ARG cc_start: 0.9152 (tpp-160) cc_final: 0.8604 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: F   73 THR cc_start: 0.9612 (m) cc_final: 0.9330 (p)
REVERT: F   88 TYR cc_start: 0.9114 (m-10) cc_final: 0.8871 (m-10)
REVERT: G   57 TYR cc_start: 0.8874 (t80) cc_final: 0.8299 (t80)
REVERT: G   64 GLU cc_start: 0.9089 (tt0) cc_final: 0.8842 (pt0)
REVERT: G   89 ASN cc_start: 0.9415 (m-40) cc_final: 0.9031 (m110)
REVERT: G   90 ASP cc_start: 0.8431 (t0) cc_final: 0.7842 (t0)
REVERT: G   92 GLU cc_start: 0.8992 (mp0) cc_final: 0.8483 (pm20)
REVERT: H   46 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9162 (mmmt)
REVERT: H   93 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8008 (mm-30)
REVERT: H  109 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8621 (m-70)
REVERT: H  113 GLU cc_start: 0.9217 (tp30) cc_final: 0.8849 (tt0)
  outliers start: 10
  outliers final: 5
  residues processed: 198
  average time/residue: 0.0996
  time to fit residues: 27.9659
Evaluate side-chains
  188 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 182
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
E  55 GLN
E  93 GLN
G  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.061700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.039644 restraints weight = 53243.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.040736 restraints weight = 28223.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.041423 restraints weight = 20497.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.041802 restraints weight = 17442.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.041987 restraints weight = 16039.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11330  Z= 0.244
  Angle     :  0.651   8.043  16385  Z= 0.374
  Chirality :  0.036   0.182   1874
  Planarity :  0.004   0.044   1197
  Dihedral  : 31.567 179.539   3499
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.94 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.31), residues: 681
  helix:  2.56 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.76 (0.44), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  42 
 TYR   0.026   0.002   TYR C  57 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (11330)
  covalent geometry    : angle       0.65062 (16385)
  hydrogen bonds       : bond        0.04740 (  706)
  hydrogen bonds       : angle       3.21275 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9096 (mt0) cc_final: 0.8603 (mt0)
REVERT: B   84 MET cc_start: 0.9141 (mmm) cc_final: 0.8580 (mmm)
REVERT: B   88 TYR cc_start: 0.9017 (m-80) cc_final: 0.8697 (m-80)
REVERT: C   38 ASN cc_start: 0.8373 (t0) cc_final: 0.7734 (t0)
REVERT: C   73 ASN cc_start: 0.9004 (t0) cc_final: 0.8597 (t0)
REVERT: C  104 GLN cc_start: 0.8599 (mp10) cc_final: 0.7874 (mp10)
REVERT: D   46 LYS cc_start: 0.9450 (mmtp) cc_final: 0.9119 (mmmt)
REVERT: D   68 ASP cc_start: 0.9068 (t70) cc_final: 0.8724 (t0)
REVERT: D   71 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: D  120 LYS cc_start: 0.9543 (ttpt) cc_final: 0.9180 (ttpp)
REVERT: E   79 LYS cc_start: 0.8821 (tmtt) cc_final: 0.8177 (tmtt)
REVERT: E  105 GLU cc_start: 0.8635 (tt0) cc_final: 0.8376 (tp30)
REVERT: E  123 ASP cc_start: 0.8755 (m-30) cc_final: 0.8279 (m-30)
REVERT: E  125 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: F   39 ARG cc_start: 0.9181 (tpp-160) cc_final: 0.8622 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8513 (mt-10)
REVERT: F   73 THR cc_start: 0.9630 (m) cc_final: 0.9375 (p)
REVERT: F   88 TYR cc_start: 0.9133 (m-10) cc_final: 0.8824 (m-10)
REVERT: G   38 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (m-40)
REVERT: G   57 TYR cc_start: 0.8990 (t80) cc_final: 0.8740 (t80)
REVERT: G   64 GLU cc_start: 0.9096 (tt0) cc_final: 0.8890 (pt0)
REVERT: G   89 ASN cc_start: 0.9421 (m-40) cc_final: 0.9047 (m110)
REVERT: G   90 ASP cc_start: 0.8600 (t0) cc_final: 0.7956 (t0)
REVERT: G   92 GLU cc_start: 0.9010 (mp0) cc_final: 0.8465 (pm20)
REVERT: H   46 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9169 (mmmt)
REVERT: H   93 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8099 (mm-30)
REVERT: H  109 HIS cc_start: 0.9261 (OUTLIER) cc_final: 0.8601 (m-70)
  outliers start: 16
  outliers final: 12
  residues processed: 188
  average time/residue: 0.0962
  time to fit residues: 25.8429
Evaluate side-chains
  189 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
E  93 GLN
G  38 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.063440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.041440 restraints weight = 52301.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.042570 restraints weight = 27580.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.043289 restraints weight = 19829.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.043692 restraints weight = 16741.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.043876 restraints weight = 15382.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11330  Z= 0.166
  Angle     :  0.628   8.899  16385  Z= 0.362
  Chirality :  0.035   0.169   1874
  Planarity :  0.004   0.044   1197
  Dihedral  : 31.364 177.643   3499
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 27.46 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.31), residues: 681
  helix:  2.59 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.63 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  99 
 TYR   0.025   0.002   TYR C  57 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11330)
  covalent geometry    : angle       0.62814 (16385)
  hydrogen bonds       : bond        0.04167 (  706)
  hydrogen bonds       : angle       3.04065 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9021 (mt0) cc_final: 0.8715 (mt0)
REVERT: C   73 ASN cc_start: 0.8940 (t0) cc_final: 0.8452 (t0)
REVERT: C  104 GLN cc_start: 0.8386 (mp10) cc_final: 0.7747 (mp10)
REVERT: D   46 LYS cc_start: 0.9486 (mmtp) cc_final: 0.9083 (mmmt)
REVERT: D   68 ASP cc_start: 0.9091 (t70) cc_final: 0.8845 (t70)
REVERT: D   71 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8573 (tm-30)
REVERT: D  120 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9106 (ttpp)
REVERT: E   79 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8002 (tmtt)
REVERT: E   80 THR cc_start: 0.8824 (p) cc_final: 0.8393 (t)
REVERT: E  125 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: F   39 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8559 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: F   73 THR cc_start: 0.9618 (m) cc_final: 0.9335 (p)
REVERT: F   88 TYR cc_start: 0.9140 (m-10) cc_final: 0.8842 (m-10)
REVERT: G   38 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8536 (m-40)
REVERT: G   57 TYR cc_start: 0.8935 (t80) cc_final: 0.8368 (t80)
REVERT: G   64 GLU cc_start: 0.9094 (tt0) cc_final: 0.8850 (pt0)
REVERT: G   89 ASN cc_start: 0.9434 (m-40) cc_final: 0.9092 (m110)
REVERT: G   90 ASP cc_start: 0.8454 (t0) cc_final: 0.7876 (t0)
REVERT: G   92 GLU cc_start: 0.9001 (mp0) cc_final: 0.8572 (pm20)
REVERT: H   46 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9166 (mmmt)
REVERT: H   93 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8102 (mm-30)
REVERT: H  109 HIS cc_start: 0.9235 (OUTLIER) cc_final: 0.8610 (m-70)
REVERT: H  113 GLU cc_start: 0.9190 (tp30) cc_final: 0.8828 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 195
  average time/residue: 0.0948
  time to fit residues: 26.1693
Evaluate side-chains
  189 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0170
   chunk 69 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.062467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.040676 restraints weight = 53687.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.041756 restraints weight = 28761.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.042412 restraints weight = 21033.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.042795 restraints weight = 18004.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.042985 restraints weight = 16577.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11330  Z= 0.207
  Angle     :  0.654   9.013  16385  Z= 0.374
  Chirality :  0.036   0.198   1874
  Planarity :  0.004   0.042   1197
  Dihedral  : 31.387 178.966   3499
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 27.81 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.31), residues: 681
  helix:  2.60 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.69 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  92 
 TYR   0.026   0.002   TYR C  57 
 PHE   0.010   0.002   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (11330)
  covalent geometry    : angle       0.65404 (16385)
  hydrogen bonds       : bond        0.04424 (  706)
  hydrogen bonds       : angle       3.12893 ( 1782)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 179
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8019 (mmm-85)
REVERT: A   85 GLN cc_start: 0.9070 (mt0) cc_final: 0.8713 (mt0)
REVERT: C   73 ASN cc_start: 0.8978 (t0) cc_final: 0.8476 (t0)
REVERT: C  104 GLN cc_start: 0.8435 (mp10) cc_final: 0.7773 (mp10)
REVERT: D   46 LYS cc_start: 0.9480 (mmtp) cc_final: 0.9042 (mmmt)
REVERT: D   68 ASP cc_start: 0.9078 (t70) cc_final: 0.8788 (t70)
REVERT: D   71 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: D  120 LYS cc_start: 0.9516 (ttpt) cc_final: 0.9149 (ttpp)
REVERT: E   79 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8138 (tmtt)
REVERT: E   80 THR cc_start: 0.8893 (p) cc_final: 0.8407 (t)
REVERT: E   93 GLN cc_start: 0.9046 (tp40) cc_final: 0.8783 (tp40)
REVERT: E  123 ASP cc_start: 0.8797 (m-30) cc_final: 0.8280 (m-30)
REVERT: E  125 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8409 (tm-30)
REVERT: F   39 ARG cc_start: 0.9169 (tpp-160) cc_final: 0.8620 (tpp-160)
REVERT: F   43 VAL cc_start: 0.9701 (t) cc_final: 0.9462 (p)
REVERT: F   63 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: F   73 THR cc_start: 0.9620 (m) cc_final: 0.9351 (p)
REVERT: F   88 TYR cc_start: 0.9165 (m-10) cc_final: 0.8856 (m-10)
REVERT: G   57 TYR cc_start: 0.8969 (t80) cc_final: 0.8405 (t80)
REVERT: G   89 ASN cc_start: 0.9444 (m-40) cc_final: 0.9108 (m110)
REVERT: G   90 ASP cc_start: 0.8492 (t0) cc_final: 0.7905 (t0)
REVERT: G   92 GLU cc_start: 0.9046 (mp0) cc_final: 0.8578 (pm20)
REVERT: H   46 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9143 (mmmt)
REVERT: H   93 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: H  109 HIS cc_start: 0.9276 (OUTLIER) cc_final: 0.8662 (m-70)
REVERT: H  113 GLU cc_start: 0.9199 (tp30) cc_final: 0.8842 (tt0)
  outliers start: 10
  outliers final: 6
  residues processed: 183
  average time/residue: 0.0944
  time to fit residues: 24.5069
Evaluate side-chains
  184 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.062265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.040607 restraints weight = 53939.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.041708 restraints weight = 29150.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.042394 restraints weight = 21164.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042777 restraints weight = 17939.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.042897 restraints weight = 16509.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11330  Z= 0.214
  Angle     :  0.663  12.114  16385  Z= 0.377
  Chirality :  0.036   0.215   1874
  Planarity :  0.004   0.043   1197
  Dihedral  : 31.383 179.776   3499
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 28.32 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.31), residues: 681
  helix:  2.58 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.69 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  92 
 TYR   0.022   0.002   TYR C  57 
 PHE   0.010   0.002   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (11330)
  covalent geometry    : angle       0.66338 (16385)
  hydrogen bonds       : bond        0.04487 (  706)
  hydrogen bonds       : angle       3.14246 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1718.15 seconds
wall clock time: 30 minutes 16.15 seconds (1816.15 seconds total)