Starting phenix.real_space_refine
on Sat Aug 23 14:05:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8peo_17633/08_2025/8peo_17633.cif"
  }
  resolution = 2.69
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      13      5.16       5
     C    7171      2.51       5
     N    2399      2.21       5
     O    2958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12835
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Chain breaks: 1
    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: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 694
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 710
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 11, 'TRANS': 74}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M2L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.34, per 1000 atoms: 0.18
  Number of scatterers: 12835
  At special positions: 0
  Unit cell: (91.696, 119.205, 138.378, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P     294     15.00
     O    2958      8.00
     N    2399      7.00
     C    7171      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 277.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      64.5% alpha, 4.8% beta
      146 base pairs and 270 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.569A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.613A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.858A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.569A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.807A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.575A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.801A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.508A  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
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.794A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.602A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.397A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.112A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 76 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.720A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.477A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.143A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.343A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.210A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53
      removed outlier: 3.839A  pdb=" N   GLU K  49 " --> pdb=" O   PHE K  44 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      374 hydrogen bonds
      748 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      270 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 0.97 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: 2228
        1.33 -     1.45: 4599
        1.45 -     1.57: 6234
        1.57 -     1.69: 586
        1.69 -     1.82: 26
  Bond restraints: 13673
  Sorted by residual:
  bond pdb=" N   ARG E 129 "
       pdb=" CA  ARG E 129 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.20e-02 6.94e+03 5.59e+00
  bond pdb=" N   ASP E 123 "
       pdb=" CA  ASP E 123 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.20e-02 6.94e+03 5.49e+00
  bond pdb=" C   TRP K  21 "
       pdb=" N   PRO K  22 "
    ideal  model  delta    sigma   weight residual
    1.332  1.358 -0.026 1.12e-02 7.97e+03 5.43e+00
  bond pdb=" N   ARG B  36 "
       pdb=" CA  ARG B  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.20e-02 6.94e+03 5.09e+00
  bond pdb=" P    DG I -49 "
       pdb=" OP1  DG I -49 "
    ideal  model  delta    sigma   weight residual
    1.480  1.521 -0.041 2.00e-02 2.50e+03 4.22e+00
  ... (remaining 13668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 18841
        1.76 -     3.52: 796
        3.52 -     5.28: 64
        5.28 -     7.03: 15
        7.03 -     8.79: 5
  Bond angle restraints: 19721
  Sorted by residual:
  angle pdb=" C   ILE B  34 "
        pdb=" N   ARG B  35 "
        pdb=" CA  ARG B  35 "
      ideal   model   delta    sigma   weight residual
     120.29  114.32    5.97 1.42e+00 4.96e-01 1.77e+01
  angle pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
        pdb=" CG  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.60  116.80   -4.20 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" CA  ASN C  73 "
        pdb=" CB  ASN C  73 "
        pdb=" CG  ASN C  73 "
      ideal   model   delta    sigma   weight residual
     112.60  116.63   -4.03 1.00e+00 1.00e+00 1.62e+01
  angle pdb=" CA  GLU D  68 "
        pdb=" CB  GLU D  68 "
        pdb=" CG  GLU D  68 "
      ideal   model   delta    sigma   weight residual
     114.10  121.58   -7.48 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" C   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     110.56  116.29   -5.73 1.69e+00 3.50e-01 1.15e+01
  ... (remaining 19716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 5770
       35.44 -    70.87: 1661
       70.87 -   106.31: 37
      106.31 -   141.74: 3
      141.74 -   177.18: 4
  Dihedral angle restraints: 7475
    sinusoidal: 5003
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CD  M2L A 201 "
           pdb=" CE  M2L A 201 "
           pdb=" NZ  M2L A 201 "
           pdb=" CM1 M2L A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.23  -97.71  163.94     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" C4'  DT J  69 "
           pdb=" C3'  DT J  69 "
           pdb=" O3'  DT J  69 "
           pdb=" P    DC J  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.82  177.18     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J  68 "
           pdb=" C3'  DC J  68 "
           pdb=" O3'  DC J  68 "
           pdb=" P    DT J  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   24.39 -164.39     1      3.50e+01 8.16e-04 1.54e+01
  ... (remaining 7472 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 2154
       0.104 -    0.208: 70
       0.208 -    0.313: 1
       0.313 -    0.417: 0
       0.417 -    0.521: 4
  Chirality restraints: 2229
  Sorted by residual:
  chirality pdb=" P    DG J  50 "
            pdb=" OP1  DG J  50 "
            pdb=" OP2  DG J  50 "
            pdb=" O5'  DG J  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.87   -0.52 2.00e-01 2.50e+01 6.78e+00
  chirality pdb=" P    DC J  49 "
            pdb=" OP1  DC J  49 "
            pdb=" OP2  DC J  49 "
            pdb=" O5'  DC J  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.86   -0.52 2.00e-01 2.50e+01 6.67e+00
  chirality pdb=" P    DC I -50 "
            pdb=" OP1  DC I -50 "
            pdb=" OP2  DC I -50 "
            pdb=" O5'  DC I -50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.86   -0.52 2.00e-01 2.50e+01 6.65e+00
  ... (remaining 2226 not shown)

  Planarity restraints: 1477
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  73 "   -0.019 2.00e-02 2.50e+03   3.88e-02 1.51e+01
        pdb=" C   ASN G  73 "    0.067 2.00e-02 2.50e+03
        pdb=" O   ASN G  73 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LYS G  74 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  69 "   -0.040 2.00e-02 2.50e+03   2.41e-02 1.31e+01
        pdb=" N1   DC I  69 "    0.057 2.00e-02 2.50e+03
        pdb=" C2   DC I  69 "   -0.013 2.00e-02 2.50e+03
        pdb=" O2   DC I  69 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  69 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I  69 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC I  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I  69 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  49 "    0.030 2.00e-02 2.50e+03   2.39e-02 1.28e+01
        pdb=" N1   DC I  49 "   -0.057 2.00e-02 2.50e+03
        pdb=" C2   DC I  49 "    0.028 2.00e-02 2.50e+03
        pdb=" O2   DC I  49 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC I  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I  49 "    0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  49 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DC I  49 "    0.006 2.00e-02 2.50e+03
        pdb=" C6   DC I  49 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1474 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1279
        2.74 -     3.28: 10720
        3.28 -     3.82: 25198
        3.82 -     4.36: 30038
        4.36 -     4.90: 43095
  Nonbonded interactions: 110330
  Sorted by model distance:
  nonbonded pdb=" O   GLU K  66 "
            pdb=" NZ  LYS K  70 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" N   GLU A  59 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NZ  LYS H  43 "
            pdb=" O   THR H  49 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   TRP K  82 "
            pdb=" ND2 ASN K  86 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.254 3.040
  ... (remaining 110325 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' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.190
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.870
  Find NCS groups from input model:        0.100
  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:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
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   0.102  13675  Z= 0.263
  Angle     :  0.772   8.793  19721  Z= 0.458
  Chirality :  0.051   0.521   2229
  Planarity :  0.006   0.119   1477
  Dihedral  : 29.822 177.176   5877
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 20.20 %
    Favored  : 79.66 %
  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 aren not related in a simple way.
  whole:  0.99 (0.29), residues: 831
  helix:  1.68 (0.22), residues: 548
  sheet: -2.59 (0.96), residues: 23
  loop : -1.27 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  35 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.014   0.002   PHE K   5 
 TRP   0.019   0.003   TRP K  82 
 HIS   0.007   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (13673)
  covalent geometry    : angle       0.77216 (19721)
  hydrogen bonds       : bond        0.12696 (  785)
  hydrogen bonds       : angle       3.94289 ( 1960)
  Misc. bond           : bond        0.10209 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.7683
  time to fit residues: 135.1214
Evaluate side-chains
  113 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
K  20 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.076428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.053936 restraints weight = 35829.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.57
r_work: 0.2817 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13675  Z= 0.179
  Angle     :  0.604  10.622  19721  Z= 0.358
  Chirality :  0.036   0.131   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 31.245 176.537   4163
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.18 %
    Favored  : 77.14 %
  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 aren not related in a simple way.
  whole:  1.94 (0.29), residues: 831
  helix:  2.27 (0.22), residues: 563
  sheet: -1.53 (1.18), residues: 21
  loop : -0.83 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  83 
 TYR   0.009   0.001   TYR K  68 
 PHE   0.012   0.002   PHE K   5 
 TRP   0.007   0.001   TRP K  21 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (13673)
  covalent geometry    : angle       0.60408 (19721)
  hydrogen bonds       : bond        0.04118 (  785)
  hydrogen bonds       : angle       2.83248 ( 1960)
  Misc. bond           : bond        0.00060 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   45 PHE cc_start: 0.7740 (m-80) cc_final: 0.7522 (m-10)
REVERT: K   63 GLU cc_start: 0.9042 (tp30) cc_final: 0.8716 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 132
  average time/residue: 0.7030
  time to fit residues: 98.2448
Evaluate side-chains
  122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 118
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
D  44 GLN
G 104 GLN
G 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.071183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.048230 restraints weight = 36333.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 1.62
r_work: 0.2649 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2534 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9015
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059  13675  Z= 0.336
  Angle     :  0.673  10.154  19721  Z= 0.396
  Chirality :  0.043   0.144   2229
  Planarity :  0.005   0.039   1477
  Dihedral  : 31.373 175.740   4163
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.06 %
    Favored  : 77.00 %
  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 aren not related in a simple way.
  whole:  1.82 (0.28), residues: 831
  helix:  2.22 (0.22), residues: 555
  sheet: -2.08 (1.02), residues: 23
  loop : -0.79 (0.34), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  83 
 TYR   0.015   0.002   TYR K  61 
 PHE   0.017   0.002   PHE K   5 
 TRP   0.007   0.002   TRP K  21 
 HIS   0.003   0.001   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 (13673)
  covalent geometry    : angle       0.67321 (19721)
  hydrogen bonds       : bond        0.05912 (  785)
  hydrogen bonds       : angle       3.03008 ( 1960)
  Misc. bond           : bond        0.00046 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   31 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8928 (mtpm)
REVERT: D   68 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8622 (tm-30)
REVERT: E   97 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8596 (mp0)
REVERT: E  120 MET cc_start: 0.9243 (mtt) cc_final: 0.8984 (mtt)
REVERT: G   73 ASN cc_start: 0.9042 (t0) cc_final: 0.8677 (t0)
REVERT: K   63 GLU cc_start: 0.8986 (tp30) cc_final: 0.8732 (tm-30)
REVERT: K   81 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7876 (mp)
  outliers start: 21
  outliers final: 8
  residues processed: 130
  average time/residue: 0.6887
  time to fit residues: 94.7482
Evaluate side-chains
  126 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   81 LEU
Chi-restraints excluded: chain K residue   90 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.072424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.049558 restraints weight = 36131.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 1.58
r_work: 0.2686 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13675  Z= 0.210
  Angle     :  0.596  10.169  19721  Z= 0.355
  Chirality :  0.037   0.125   2229
  Planarity :  0.004   0.039   1477
  Dihedral  : 30.932 177.272   4163
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.60 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.29), residues: 831
  helix:  2.48 (0.22), residues: 555
  sheet: -2.37 (0.87), residues: 25
  loop : -0.66 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  83 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.008   0.001   PHE K   5 
 TRP   0.003   0.001   TRP K  21 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (13673)
  covalent geometry    : angle       0.59650 (19721)
  hydrogen bonds       : bond        0.04657 (  785)
  hydrogen bonds       : angle       2.82054 ( 1960)
  Misc. bond           : bond        0.00011 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8594 (tm-30)
REVERT: E  120 MET cc_start: 0.9242 (mtt) cc_final: 0.8986 (mtt)
REVERT: F   20 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6677 (mmmt)
REVERT: G   73 ASN cc_start: 0.9034 (t0) cc_final: 0.8621 (t0)
REVERT: K    9 ASP cc_start: 0.7701 (t0) cc_final: 0.7468 (p0)
REVERT: K   58 ILE cc_start: 0.5795 (OUTLIER) cc_final: 0.5547 (mt)
REVERT: K   63 GLU cc_start: 0.8956 (tp30) cc_final: 0.8715 (tm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 132
  average time/residue: 0.7636
  time to fit residues: 106.5516
Evaluate side-chains
  126 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   90 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
** K  72 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 = 0.3432 r_free = 0.3432 target = 0.071975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.049088 restraints weight = 36182.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 1.58
r_work: 0.2672 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2556 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13675  Z= 0.239
  Angle     :  0.602   8.363  19721  Z= 0.359
  Chirality :  0.038   0.123   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.778 177.571   4163
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.46 %
    Favored  : 76.16 %
  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 aren not related in a simple way.
  whole:  2.20 (0.29), residues: 831
  helix:  2.52 (0.22), residues: 557
  sheet: -2.63 (0.87), residues: 25
  loop : -0.59 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  83 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.011   0.001   PHE K   5 
 TRP   0.002   0.001   TRP K  82 
 HIS   0.003   0.001   HIS K  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (13673)
  covalent geometry    : angle       0.60215 (19721)
  hydrogen bonds       : bond        0.04860 (  785)
  hydrogen bonds       : angle       2.81415 ( 1960)
  Misc. bond           : bond        0.00018 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8626 (tm-30)
REVERT: E   97 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (mp0)
REVERT: E  120 MET cc_start: 0.9237 (mtt) cc_final: 0.8982 (mtt)
REVERT: F   20 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6650 (mmmt)
REVERT: G   73 ASN cc_start: 0.9059 (t0) cc_final: 0.8615 (t0)
REVERT: K   63 GLU cc_start: 0.8948 (tp30) cc_final: 0.8713 (tm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 129
  average time/residue: 0.7468
  time to fit residues: 102.0718
Evaluate side-chains
  128 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   90 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 93 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
** K  20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 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 = 0.3446 r_free = 0.3446 target = 0.072603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.049808 restraints weight = 35605.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.56
r_work: 0.2693 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2577 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8980
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13675  Z= 0.167
  Angle     :  0.597   9.742  19721  Z= 0.353
  Chirality :  0.035   0.124   2229
  Planarity :  0.004   0.061   1477
  Dihedral  : 30.794 177.704   4163
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.60 %
    Favored  : 76.30 %
  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 aren not related in a simple way.
  whole:  2.32 (0.29), residues: 831
  helix:  2.63 (0.22), residues: 557
  sheet: -2.64 (0.81), residues: 25
  loop : -0.60 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  74 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.009   0.001   PHE K   5 
 TRP   0.003   0.001   TRP K  82 
 HIS   0.005   0.001   HIS K  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13673)
  covalent geometry    : angle       0.59694 (19721)
  hydrogen bonds       : bond        0.04459 (  785)
  hydrogen bonds       : angle       2.77211 ( 1960)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8628 (tm-30)
REVERT: E   97 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8620 (mp0)
REVERT: E  120 MET cc_start: 0.9225 (mtt) cc_final: 0.8981 (mtt)
REVERT: F   20 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6712 (mmmt)
REVERT: G   73 ASN cc_start: 0.9043 (t0) cc_final: 0.8586 (t0)
REVERT: K   57 ASP cc_start: 0.6560 (p0) cc_final: 0.6336 (p0)
REVERT: K   58 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5565 (mt)
REVERT: K   63 GLU cc_start: 0.8948 (tp30) cc_final: 0.8721 (tm-30)
  outliers start: 15
  outliers final: 6
  residues processed: 126
  average time/residue: 0.7490
  time to fit residues: 99.8761
Evaluate side-chains
  123 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
K  20 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.072422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.049653 restraints weight = 35862.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.56
r_work: 0.2691 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13675  Z= 0.212
  Angle     :  0.593   9.086  19721  Z= 0.352
  Chirality :  0.036   0.122   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.676 178.038   4163
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.30 %
    Favored  : 75.74 %
  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 aren not related in a simple way.
  whole:  2.42 (0.29), residues: 831
  helix:  2.69 (0.22), residues: 557
  sheet: -2.47 (0.85), residues: 25
  loop : -0.52 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.010   0.001   PHE K  52 
 TRP   0.002   0.001   TRP K  21 
 HIS   0.002   0.001   HIS K  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (13673)
  covalent geometry    : angle       0.59304 (19721)
  hydrogen bonds       : bond        0.04512 (  785)
  hydrogen bonds       : angle       2.73393 ( 1960)
  Misc. bond           : bond        0.00018 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8596 (tm-30)
REVERT: E  120 MET cc_start: 0.9222 (mtt) cc_final: 0.8963 (mtt)
REVERT: F   20 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6714 (mmmt)
REVERT: G   73 ASN cc_start: 0.9054 (t0) cc_final: 0.8566 (t0)
REVERT: K   58 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5610 (mt)
REVERT: K   63 GLU cc_start: 0.8940 (tp30) cc_final: 0.8711 (tm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 124
  average time/residue: 0.6987
  time to fit residues: 91.8232
Evaluate side-chains
  122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 90 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.5884

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.071733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.048950 restraints weight = 35621.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 1.55
r_work: 0.2671 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2555 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13675  Z= 0.235
  Angle     :  0.611   8.696  19721  Z= 0.360
  Chirality :  0.038   0.124   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.707 178.376   4163
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.28 %
    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 aren not related in a simple way.
  whole:  2.38 (0.29), residues: 831
  helix:  2.62 (0.22), residues: 557
  sheet: -2.33 (0.89), residues: 25
  loop : -0.45 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  74 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.014   0.001   PHE K   5 
 TRP   0.002   0.001   TRP K  21 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (13673)
  covalent geometry    : angle       0.61061 (19721)
  hydrogen bonds       : bond        0.04846 (  785)
  hydrogen bonds       : angle       2.79134 ( 1960)
  Misc. bond           : bond        0.00025 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8632 (tm-30)
REVERT: E   39 HIS cc_start: 0.7862 (t70) cc_final: 0.6484 (m90)
REVERT: E  120 MET cc_start: 0.9207 (mtt) cc_final: 0.8972 (mtt)
REVERT: F   20 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6708 (mmmt)
REVERT: G   73 ASN cc_start: 0.9038 (t0) cc_final: 0.8585 (t0)
REVERT: K   63 GLU cc_start: 0.8889 (tp30) cc_final: 0.8685 (tm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 121
  average time/residue: 0.7119
  time to fit residues: 91.2817
Evaluate side-chains
  119 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.072235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.049444 restraints weight = 35807.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 1.56
r_work: 0.2684 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2569 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8977
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13675  Z= 0.185
  Angle     :  0.610   9.601  19721  Z= 0.358
  Chirality :  0.036   0.195   2229
  Planarity :  0.004   0.042   1477
  Dihedral  : 30.714 178.443   4163
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 24.12 %
    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 aren not related in a simple way.
  whole:  2.45 (0.29), residues: 831
  helix:  2.66 (0.22), residues: 557
  sheet: -2.28 (0.85), residues: 25
  loop : -0.40 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  74 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.011   0.001   PHE K   5 
 TRP   0.001   0.000   TRP K  82 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13673)
  covalent geometry    : angle       0.60986 (19721)
  hydrogen bonds       : bond        0.04605 (  785)
  hydrogen bonds       : angle       2.76911 ( 1960)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8605 (tm-30)
REVERT: E   39 HIS cc_start: 0.7865 (t70) cc_final: 0.6501 (m90)
REVERT: E  120 MET cc_start: 0.9224 (mtt) cc_final: 0.8982 (mtt)
REVERT: F   20 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6700 (mmmt)
REVERT: G   73 ASN cc_start: 0.9057 (t0) cc_final: 0.8590 (t0)
REVERT: K   63 GLU cc_start: 0.8911 (tp30) cc_final: 0.8694 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 121
  average time/residue: 0.6919
  time to fit residues: 88.6478
Evaluate side-chains
  121 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0010
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
** K  72 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 = 0.3438 r_free = 0.3438 target = 0.072219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.049462 restraints weight = 35873.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 1.55
r_work: 0.2687 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8976
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13675  Z= 0.184
  Angle     :  0.605  10.430  19721  Z= 0.356
  Chirality :  0.036   0.133   2229
  Planarity :  0.004   0.042   1477
  Dihedral  : 30.691 178.446   4163
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.98 %
    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 aren not related in a simple way.
  whole:  2.48 (0.29), residues: 831
  helix:  2.69 (0.22), residues: 557
  sheet: -2.28 (0.85), residues: 25
  loop : -0.39 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  74 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.010   0.001   PHE K   5 
 TRP   0.001   0.000   TRP K  82 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (13673)
  covalent geometry    : angle       0.60470 (19721)
  hydrogen bonds       : bond        0.04536 (  785)
  hydrogen bonds       : angle       2.75057 ( 1960)
  Misc. bond           : bond        0.00007 (    2)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8614 (tm-30)
REVERT: E   39 HIS cc_start: 0.7869 (t70) cc_final: 0.6497 (m90)
REVERT: E  120 MET cc_start: 0.9225 (mtt) cc_final: 0.8981 (mtt)
REVERT: F   20 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6715 (mmmt)
REVERT: G   73 ASN cc_start: 0.9048 (t0) cc_final: 0.8579 (t0)
REVERT: K   63 GLU cc_start: 0.8906 (tp30) cc_final: 0.8691 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 121
  average time/residue: 0.7845
  time to fit residues: 100.4136
Evaluate side-chains
  122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue    1 MET
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   40 LEU
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
G 104 GLN
** K  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.072439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.049655 restraints weight = 35744.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.56
r_work: 0.2691 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13675  Z= 0.178
  Angle     :  0.601  10.381  19721  Z= 0.354
  Chirality :  0.035   0.129   2229
  Planarity :  0.004   0.043   1477
  Dihedral  : 30.682 178.466   4163
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 23.70 %
    Favored  : 74.89 %
  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 aren not related in a simple way.
  whole:  2.49 (0.29), residues: 831
  helix:  2.70 (0.22), residues: 557
  sheet: -2.23 (0.85), residues: 25
  loop : -0.43 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  74 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.010   0.001   PHE K  52 
 TRP   0.001   0.000   TRP K  82 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13673)
  covalent geometry    : angle       0.60129 (19721)
  hydrogen bonds       : bond        0.04466 (  785)
  hydrogen bonds       : angle       2.73897 ( 1960)
  Misc. bond           : bond        0.00013 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4457.30 seconds
wall clock time: 76 minutes 19.22 seconds (4579.22 seconds total)