Starting phenix.real_space_refine
on Tue Jul 29 19:42:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2025/7v90_31806.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      14      5.16       5
     C    6737      2.51       5
     N    2288      2.21       5
     O    2821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12148
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 824
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 783
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "E"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 825
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 773
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "I"
      Number of atoms: 3067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 3067
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2872
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 7.50, per 1000 atoms: 0.62
  Number of scatterers: 12148
  At special positions: 0
  Unit cell: (115.83, 113.256, 124.41, 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     288     15.00
     O    2821      8.00
     N    2288      7.00
     C    6737      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: 3.01
  Conformation dependent library (CDL) restraints added in 904.0 milliseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1458

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      69.4% alpha, 2.3% beta
      123 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 5.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 64 through 75
      removed outlier: 3.633A  pdb=" N   ALA A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.575A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.977A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 120 through 126'
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.568A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 27
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.796A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.794A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B  94 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.467A  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 95
      removed outlier: 4.057A  pdb=" N   ASN C  94 " --> pdb=" O   ASP C  90 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 90 through 95'
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.699A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.566A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.667A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.745A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.644A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 76
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.680A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.597A  pdb=" N   LYS H  40 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.759A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.720A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.004A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.447A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.439A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 7.007A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.102A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.665A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78

    380 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      306 hydrogen bonds
      612 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 4.63

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1411
        1.32 -     1.44: 4779
        1.44 -     1.56: 6161
        1.56 -     1.69: 576
        1.69 -     1.81: 24
  Bond restraints: 12951
  Sorted by residual:
  bond pdb=" N   ASP C  90 "
       pdb=" CA  ASP C  90 "
    ideal  model  delta    sigma   weight residual
    1.456  1.529 -0.074 1.25e-02 6.40e+03 3.47e+01
  bond pdb=" CA  SER D  35 "
       pdb=" CB  SER D  35 "
    ideal  model  delta    sigma   weight residual
    1.535  1.480  0.055 1.58e-02 4.01e+03 1.19e+01
  bond pdb=" O3'  DG I  12 "
       pdb=" P    DG I  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.658 -0.051 1.50e-02 4.44e+03 1.15e+01
  bond pdb=" O3'  DG I -66 "
       pdb=" P    DG I -65 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" N   ARG A 129 "
       pdb=" CA  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 9.90e+00
  ... (remaining 12946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 18152
        2.16 -     4.33: 523
        4.33 -     6.49: 36
        6.49 -     8.65: 5
        8.65 -    10.81: 2
  Bond angle restraints: 18718
  Sorted by residual:
  angle pdb=" C   TYR D  34 "
        pdb=" CA  TYR D  34 "
        pdb=" CB  TYR D  34 "
      ideal   model   delta    sigma   weight residual
     112.12  103.64    8.48 1.50e+00 4.44e-01 3.20e+01
  angle pdb=" N   LEU A 126 "
        pdb=" CA  LEU A 126 "
        pdb=" C   LEU A 126 "
      ideal   model   delta    sigma   weight residual
     112.87  106.38    6.49 1.20e+00 6.94e-01 2.92e+01
  angle pdb=" N   ARG A 128 "
        pdb=" CA  ARG A 128 "
        pdb=" C   ARG A 128 "
      ideal   model   delta    sigma   weight residual
     110.80   99.99   10.81 2.13e+00 2.20e-01 2.58e+01
  angle pdb=" N   ASP C  90 "
        pdb=" CA  ASP C  90 "
        pdb=" C   ASP C  90 "
      ideal   model   delta    sigma   weight residual
     110.35  117.18   -6.83 1.36e+00 5.41e-01 2.52e+01
  angle pdb=" N   PHE F 100 "
        pdb=" CA  PHE F 100 "
        pdb=" C   PHE F 100 "
      ideal   model   delta    sigma   weight residual
     113.18  107.27    5.91 1.21e+00 6.83e-01 2.38e+01
  ... (remaining 18713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.87: 5636
       30.87 -    61.74: 1444
       61.74 -    92.61: 24
       92.61 -   123.48: 0
      123.48 -   154.35: 1
  Dihedral angle restraints: 7105
    sinusoidal: 4844
      harmonic: 2261
  Sorted by residual:
  dihedral pdb=" N   ASP C  90 "
           pdb=" C   ASP C  90 "
           pdb=" CA  ASP C  90 "
           pdb=" CB  ASP C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.60  -12.80     0      2.50e+00 1.60e-01 2.62e+01
  dihedral pdb=" C   ASP C  90 "
           pdb=" N   ASP C  90 "
           pdb=" CA  ASP C  90 "
           pdb=" CB  ASP C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.28   10.68     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" C   ARG C  20 "
           pdb=" N   ARG C  20 "
           pdb=" CA  ARG C  20 "
           pdb=" CB  ARG C  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.22   10.62     0      2.50e+00 1.60e-01 1.81e+01
  ... (remaining 7102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1989
       0.080 -    0.160: 110
       0.160 -    0.240: 16
       0.240 -    0.320: 7
       0.320 -    0.400: 1
  Chirality restraints: 2123
  Sorted by residual:
  chirality pdb=" CA  ASP C  90 "
            pdb=" N   ASP C  90 "
            pdb=" C   ASP C  90 "
            pdb=" CB  ASP C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" CA  TYR D  34 "
            pdb=" N   TYR D  34 "
            pdb=" C   TYR D  34 "
            pdb=" CB  TYR D  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  ARG C  20 "
            pdb=" N   ARG C  20 "
            pdb=" C   ARG C  20 "
            pdb=" CB  ARG C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 2120 not shown)

  Planarity restraints: 1365
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C  90 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   ASP C  90 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ASP C  90 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU C  91 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C  88 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.90e+00
        pdb=" C   ARG C  88 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ARG C  88 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN C  89 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 125 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   GLN A 125 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 125 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 126 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1362 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1458
        2.75 -     3.29: 10271
        3.29 -     3.83: 22498
        3.83 -     4.36: 25965
        4.36 -     4.90: 39112
  Nonbonded interactions: 99304
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  87 "
            pdb=" OE1 GLU D  90 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLU D 102 "
            pdb=" ND1 HIS D 106 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   ILE A 119 "
            pdb=" OG  SER B  47 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" N2   DG I -28 "
            pdb=" N3   DC J  28 "
     model   vdw
     2.416 3.200
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP1  DC J -44 "
     model   vdw
     2.430 3.120
  ... (remaining 99299 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 36 through 134 or (resid 135 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 24 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     32.210
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
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      :  0.005   0.074  12951  Z= 0.310
  Angle     :  0.727  10.814  18718  Z= 0.489
  Chirality :  0.044   0.400   2123
  Planarity :  0.003   0.035   1365
  Dihedral  : 26.094 154.348   5647
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.71 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  5.08 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.41 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.28), residues: 765
  helix:  0.89 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.20 (0.30), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  46 
 PHE   0.021   0.001   PHE F 100 
 TYR   0.015   0.001   TYR D  34 
 ARG   0.004   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12146 (  686)
  hydrogen bonds       : angle       4.20261 ( 1746)
  covalent geometry    : bond        0.00486 (12951)
  covalent geometry    : angle       0.72728 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7694 (mttp)
REVERT: C   15 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7039 (tttp)
REVERT: D   30 ARG cc_start: 0.5004 (ptm-80) cc_final: 0.4200 (mtp85)
REVERT: F   35 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7353 (mtm-85)
REVERT: G   15 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7554 (tttt)
REVERT: H   25 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2114 (ptmt)
  outliers start: 26
  outliers final: 5
  residues processed: 141
  average time/residue: 0.4616
  time to fit residues: 80.0085
Evaluate side-chains
  71 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain E residue   36 LYS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue  100 PHE
Chi-restraints excluded: chain H residue   25 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  75 HIS
C  84 GLN
D  44 GLN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
F  75 HIS
G  84 GLN
H  92 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.164262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.119760 restraints weight = 14765.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.118208 restraints weight = 25901.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.119131 restraints weight = 23254.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12951  Z= 0.229
  Angle     :  0.631   6.707  18718  Z= 0.370
  Chirality :  0.037   0.181   2123
  Planarity :  0.005   0.049   1365
  Dihedral  : 30.286 161.287   4095
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  3.40 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  8.47 %
    Favored  : 89.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.29), residues: 765
  helix:  1.84 (0.22), residues: 523
  sheet:  None (None), residues: 0
  loop : -2.11 (0.32), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS F  75 
 PHE   0.016   0.002   PHE H  62 
 TYR   0.018   0.002   TYR F  51 
 ARG   0.009   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08048 (  686)
  hydrogen bonds       : angle       2.98367 ( 1746)
  covalent geometry    : bond        0.00522 (12951)
  covalent geometry    : angle       0.63051 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  109 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8194 (mp)
REVERT: B   79 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8146 (mttp)
REVERT: C   15 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7517 (tttp)
REVERT: D   30 ARG cc_start: 0.5915 (ptm-80) cc_final: 0.5060 (mtp180)
REVERT: H   96 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7443 (mtm180)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.3672
  time to fit residues: 44.6757
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   84 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0020
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 76 optimal weight:   10.0000
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS
D  60 ASN
F  75 HIS
H  44 GLN
H  46 HIS
H  81 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.169605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.125457 restraints weight = 14962.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.124173 restraints weight = 25345.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.125040 restraints weight = 23380.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12951  Z= 0.140
  Angle     :  0.504   5.891  18718  Z= 0.306
  Chirality :  0.032   0.168   2123
  Planarity :  0.003   0.038   1365
  Dihedral  : 29.917 161.990   4083
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.14 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  9.09 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.30), residues: 765
  helix:  2.56 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.75 (0.34), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.008   0.001   PHE F 100 
 TYR   0.008   0.001   TYR C  50 
 ARG   0.005   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04788 (  686)
  hydrogen bonds       : angle       2.48914 ( 1746)
  covalent geometry    : bond        0.00297 (12951)
  covalent geometry    : angle       0.50422 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7492 (tttp)
REVERT: D   30 ARG cc_start: 0.5828 (ptm-80) cc_final: 0.5074 (mtt180)
REVERT: F   35 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7461 (mtm110)
REVERT: H   56 MET cc_start: 0.7845 (tpp) cc_final: 0.7560 (mmt)
REVERT: H   96 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7339 (mtm180)
  outliers start: 10
  outliers final: 9
  residues processed: 88
  average time/residue: 0.3439
  time to fit residues: 39.7975
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS
G  38 ASN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.161316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.117063 restraints weight = 14659.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.115475 restraints weight = 25386.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.116423 restraints weight = 22170.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12951  Z= 0.224
  Angle     :  0.606   7.121  18718  Z= 0.359
  Chirality :  0.037   0.187   2123
  Planarity :  0.005   0.041   1365
  Dihedral  : 30.136 163.337   4083
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.17 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.30), residues: 765
  helix:  2.19 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -1.86 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.016   0.002   PHE F 100 
 TYR   0.015   0.002   TYR F  51 
 ARG   0.006   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08008 (  686)
  hydrogen bonds       : angle       2.96105 ( 1746)
  covalent geometry    : bond        0.00516 (12951)
  covalent geometry    : angle       0.60648 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8549 (t0) cc_final: 0.8309 (t0)
REVERT: D   96 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7367 (mtm180)
REVERT: H   73 GLU cc_start: 0.8603 (tp30) cc_final: 0.8370 (tp30)
REVERT: H   96 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7413 (mtm180)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.3390
  time to fit residues: 39.3324
Evaluate side-chains
  77 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 81 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
G  38 ASN
H  81 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.167805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.122856 restraints weight = 14808.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.123274 restraints weight = 27871.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.123449 restraints weight = 27132.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12951  Z= 0.141
  Angle     :  0.500   4.989  18718  Z= 0.305
  Chirality :  0.032   0.156   2123
  Planarity :  0.004   0.036   1365
  Dihedral  : 29.918 163.476   4083
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.75 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.79 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.30), residues: 765
  helix:  2.73 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.67 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE F  61 
 TYR   0.016   0.001   TYR D 118 
 ARG   0.010   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04805 (  686)
  hydrogen bonds       : angle       2.51205 ( 1746)
  covalent geometry    : bond        0.00298 (12951)
  covalent geometry    : angle       0.50031 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
REVERT: H   73 GLU cc_start: 0.8623 (tp30) cc_final: 0.8342 (tp30)
REVERT: H   96 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7331 (mtm180)
  outliers start: 10
  outliers final: 10
  residues processed: 78
  average time/residue: 0.3542
  time to fit residues: 37.3889
Evaluate side-chains
  72 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain H residue   84 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.113808 restraints weight = 14836.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.113660 restraints weight = 29818.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.114557 restraints weight = 31222.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12951  Z= 0.212
  Angle     :  0.585   5.973  18718  Z= 0.349
  Chirality :  0.036   0.166   2123
  Planarity :  0.005   0.052   1365
  Dihedral  : 30.143 163.452   4083
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.58 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 10.32 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.30), residues: 765
  helix:  2.35 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.67 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.015   0.002   PHE H  62 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.011   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07585 (  686)
  hydrogen bonds       : angle       2.88798 ( 1746)
  covalent geometry    : bond        0.00489 (12951)
  covalent geometry    : angle       0.58494 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9179 (m-80) cc_final: 0.8894 (m-80)
REVERT: B   95 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7465 (ptm160)
REVERT: E  109 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8045 (mp)
REVERT: F   35 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7442 (mtm110)
REVERT: H   73 GLU cc_start: 0.8607 (tp30) cc_final: 0.8339 (tp30)
REVERT: H   89 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7657 (ptm-80)
REVERT: H   96 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7412 (mtm180)
  outliers start: 21
  outliers final: 14
  residues processed: 84
  average time/residue: 0.3400
  time to fit residues: 37.4026
Evaluate side-chains
  81 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   89 ARG
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 68 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.166052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.122595 restraints weight = 14638.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.122035 restraints weight = 37400.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.123075 restraints weight = 34895.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12951  Z= 0.166
  Angle     :  0.528   5.058  18718  Z= 0.320
  Chirality :  0.033   0.152   2123
  Planarity :  0.004   0.044   1365
  Dihedral  : 30.049 163.535   4083
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.40 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 765
  helix:  2.57 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.58 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE H  62 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.008   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05916 (  686)
  hydrogen bonds       : angle       2.66081 ( 1746)
  covalent geometry    : bond        0.00365 (12951)
  covalent geometry    : angle       0.52818 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9159 (m-80) cc_final: 0.8938 (m-80)
REVERT: B   95 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7416 (ptm160)
REVERT: F   21 VAL cc_start: 0.4295 (OUTLIER) cc_final: 0.4002 (t)
REVERT: F   35 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7385 (mtm110)
REVERT: H   73 GLU cc_start: 0.8609 (tp30) cc_final: 0.8348 (tp30)
REVERT: H   89 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7678 (ptm-80)
REVERT: H   96 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7352 (mtm180)
  outliers start: 17
  outliers final: 11
  residues processed: 84
  average time/residue: 0.3619
  time to fit residues: 39.9038
Evaluate side-chains
  81 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   75 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   89 ARG
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 80 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0070
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.166983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.124074 restraints weight = 14772.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.123911 restraints weight = 37283.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.125004 restraints weight = 33945.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12951  Z= 0.144
  Angle     :  0.513   5.012  18718  Z= 0.314
  Chirality :  0.032   0.146   2123
  Planarity :  0.004   0.060   1365
  Dihedral  : 30.042 163.433   4083
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.53 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.17 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.31), residues: 765
  helix:  2.71 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.51 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE H  62 
 TYR   0.052   0.001   TYR D 118 
 ARG   0.008   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05531 (  686)
  hydrogen bonds       : angle       2.62132 ( 1746)
  covalent geometry    : bond        0.00301 (12951)
  covalent geometry    : angle       0.51325 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9150 (m-80) cc_final: 0.8933 (m-80)
REVERT: B   95 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7415 (ptm160)
REVERT: F   21 VAL cc_start: 0.4311 (OUTLIER) cc_final: 0.4011 (t)
REVERT: F   35 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7376 (mtm110)
REVERT: H   73 GLU cc_start: 0.8591 (tp30) cc_final: 0.8324 (tp30)
REVERT: H   89 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7707 (ptm-80)
REVERT: H   96 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7308 (mtm180)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.3584
  time to fit residues: 36.9601
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   89 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0000
   chunk 99 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 94 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS
H  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.167970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.125460 restraints weight = 14632.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.125018 restraints weight = 33867.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125963 restraints weight = 31080.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12951  Z= 0.145
  Angle     :  0.506   5.029  18718  Z= 0.309
  Chirality :  0.032   0.144   2123
  Planarity :  0.004   0.035   1365
  Dihedral  : 30.025 163.236   4083
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.33 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.31), residues: 765
  helix:  2.83 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.51 (0.35), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS E  39 
 PHE   0.008   0.001   PHE H  62 
 TYR   0.034   0.001   TYR D 118 
 ARG   0.006   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05290 (  686)
  hydrogen bonds       : angle       2.54641 ( 1746)
  covalent geometry    : bond        0.00307 (12951)
  covalent geometry    : angle       0.50576 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9138 (m-80) cc_final: 0.8818 (m-80)
REVERT: B   95 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7436 (ptm160)
REVERT: F   21 VAL cc_start: 0.4275 (OUTLIER) cc_final: 0.3999 (t)
REVERT: F   35 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7351 (mtm110)
REVERT: H   73 GLU cc_start: 0.8588 (tp30) cc_final: 0.8317 (tp30)
REVERT: H   89 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7737 (ptm-80)
REVERT: H   96 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7300 (mtm180)
  outliers start: 15
  outliers final: 12
  residues processed: 79
  average time/residue: 0.3555
  time to fit residues: 36.8820
Evaluate side-chains
  81 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   89 ARG
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.165550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.121893 restraints weight = 14565.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.121786 restraints weight = 35875.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.122796 restraints weight = 34446.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12951  Z= 0.170
  Angle     :  0.533   5.100  18718  Z= 0.322
  Chirality :  0.034   0.154   2123
  Planarity :  0.004   0.041   1365
  Dihedral  : 30.113 163.298   4083
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.02 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.31), residues: 765
  helix:  2.67 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E  39 
 PHE   0.011   0.002   PHE H  62 
 TYR   0.032   0.001   TYR D 118 
 ARG   0.010   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06294 (  686)
  hydrogen bonds       : angle       2.68472 ( 1746)
  covalent geometry    : bond        0.00379 (12951)
  covalent geometry    : angle       0.53265 (18718)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9176 (m-80) cc_final: 0.8946 (m-80)
REVERT: B   95 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7523 (ptm160)
REVERT: F   21 VAL cc_start: 0.4320 (OUTLIER) cc_final: 0.4029 (t)
REVERT: F   35 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7435 (mtm110)
REVERT: H   73 GLU cc_start: 0.8586 (tp30) cc_final: 0.8315 (tp30)
REVERT: H   89 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7708 (ptm-80)
REVERT: H   96 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7353 (mtm180)
  outliers start: 17
  outliers final: 12
  residues processed: 80
  average time/residue: 0.3579
  time to fit residues: 37.3163
Evaluate side-chains
  82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   89 ARG
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 94 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.160552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.120159 restraints weight = 14645.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.118936 restraints weight = 32050.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.119852 restraints weight = 24900.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  12951  Z= 0.281
  Angle     :  0.659   6.793  18718  Z= 0.388
  Chirality :  0.040   0.178   2123
  Planarity :  0.005   0.060   1365
  Dihedral  : 30.385 163.377   4083
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.02 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.30), residues: 765
  helix:  2.09 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.97 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.016   0.002   PHE H  62 
 TYR   0.049   0.002   TYR D 118 
 ARG   0.014   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08670 (  686)
  hydrogen bonds       : angle       3.06251 ( 1746)
  covalent geometry    : bond        0.00669 (12951)
  covalent geometry    : angle       0.65890 (18718)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3157.66 seconds
wall clock time: 55 minutes 27.70 seconds (3327.70 seconds total)