Starting phenix.real_space_refine
on Thu May 15 01:57:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8peo_17633/05_2025/8peo_17633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8peo_17633/05_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_17633/05_2025/8peo_17633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8peo_17633/05_2025/8peo_17633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8peo_17633/05_2025/8peo_17633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8peo_17633/05_2025/8peo_17633.cif"
  }
  resolution = 2.69
  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=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.28, per 1000 atoms: 0.65
  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: 3.18
  Conformation dependent library (CDL) restraints added in 936.4 milliseconds
  

  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: 5.75
  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: 4.53

  Time building geometry restraints manager: 3.68 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:             5.410
  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:                    0.140
  Process input model:                     34.220
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.740
-------------------------------------------------------------------------------
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 (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:  0.99 (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
 TRP   0.019   0.003   TRP K  82 
 HIS   0.007   0.001   HIS C  82 
 PHE   0.014   0.002   PHE K   5 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.014   0.001   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12696 (  785)
  hydrogen bonds       : angle       3.94289 ( 1960)
  covalent geometry    : bond        0.00512 (13673)
  covalent geometry    : angle       0.77216 (19721)
  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  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 2.0013
  time to fit residues: 352.4892
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  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0870
   chunk 27 optimal weight:    0.0980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.077804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.055428 restraints weight = 35947.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.57
r_work: 0.2857 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1936

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= 0.162
  Angle     :  0.591  10.747  19721  Z= 0.352
  Chirality :  0.035   0.128   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 31.217 177.299   4163
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.46 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.98 (0.29), residues: 831
  helix:  2.31 (0.22), residues: 563
  sheet: -1.55 (1.17), residues: 21
  loop : -0.82 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  21 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.009   0.001   PHE K   5 
 TYR   0.008   0.001   TYR K  68 
 ARG   0.007   0.001   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03921 (  785)
  hydrogen bonds       : angle       2.78650 ( 1960)
  covalent geometry    : bond        0.00354 (13673)
  covalent geometry    : angle       0.59123 (19721)
  Misc. bond           : bond        0.00031 (    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
  141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  105 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8739 (tppt)
REVERT: K   45 PHE cc_start: 0.7810 (m-80) cc_final: 0.7520 (m-10)
REVERT: K   63 GLU cc_start: 0.9022 (tp30) cc_final: 0.8711 (tm-30)
  outliers start: 12
  outliers final: 3
  residues processed: 133
  average time/residue: 1.6985
  time to fit residues: 240.4334
Evaluate side-chains
  122 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 85 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 102 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.0984

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.074244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.051616 restraints weight = 35695.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.56
r_work: 0.2753 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13675  Z= 0.196
  Angle     :  0.586  10.499  19721  Z= 0.350
  Chirality :  0.036   0.140   2229
  Planarity :  0.004   0.038   1477
  Dihedral  : 31.043 177.408   4163
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.62 %
    Favored  : 77.42 %
  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:  2.29 (0.29), residues: 831
  helix:  2.54 (0.22), residues: 561
  sheet: -1.28 (1.19), residues: 21
  loop : -0.68 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP K  82 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.008   0.001   PHE K   5 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.007   0.001   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04572 (  785)
  hydrogen bonds       : angle       2.75715 ( 1960)
  covalent geometry    : bond        0.00436 (13673)
  covalent geometry    : angle       0.58617 (19721)
  Misc. bond           : bond        0.00017 (    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
  137 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   31 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8816 (mppt)
REVERT: D   68 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8619 (tm-30)
REVERT: E  120 MET cc_start: 0.9220 (mtt) cc_final: 0.8979 (mtt)
REVERT: G   73 ASN cc_start: 0.8999 (t0) cc_final: 0.8633 (t0)
REVERT: K   63 GLU cc_start: 0.8982 (tp30) cc_final: 0.8750 (tm-30)
REVERT: K   74 ARG cc_start: 0.7837 (mmt90) cc_final: 0.7572 (mmt90)
  outliers start: 14
  outliers final: 8
  residues processed: 130
  average time/residue: 1.7356
  time to fit residues: 240.1168
Evaluate side-chains
  124 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 4 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.074628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.052235 restraints weight = 35497.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.55
r_work: 0.2777 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13675  Z= 0.175
  Angle     :  0.564  11.522  19721  Z= 0.337
  Chirality :  0.035   0.123   2229
  Planarity :  0.004   0.039   1477
  Dihedral  : 30.717 178.193   4163
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.04 %
    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 (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:  2.49 (0.29), residues: 831
  helix:  2.72 (0.22), residues: 557
  sheet: -1.54 (1.03), residues: 21
  loop : -0.58 (0.35), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  82 
 HIS   0.003   0.001   HIS E 113 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.008   0.001   TYR F  51 
 ARG   0.009   0.000   ARG F  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  785)
  hydrogen bonds       : angle       2.64241 ( 1960)
  covalent geometry    : bond        0.00389 (13673)
  covalent geometry    : angle       0.56410 (19721)
  Misc. bond           : bond        0.00018 (    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
  135 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8591 (tm-30)
REVERT: E  120 MET cc_start: 0.9233 (mtt) cc_final: 0.8967 (mtt)
REVERT: F   20 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6581 (mmmt)
REVERT: G   73 ASN cc_start: 0.8971 (t0) cc_final: 0.8613 (t0)
REVERT: H   90 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8138 (mp0)
REVERT: K   63 GLU cc_start: 0.8948 (tp30) cc_final: 0.8729 (tm-30)
REVERT: K   74 ARG cc_start: 0.8283 (mmt90) cc_final: 0.7833 (mmt90)
REVERT: K   83 GLU cc_start: 0.8067 (pt0) cc_final: 0.7845 (pt0)
  outliers start: 13
  outliers final: 6
  residues processed: 129
  average time/residue: 1.7725
  time to fit residues: 242.9688
Evaluate side-chains
  125 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
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   90 GLU
Chi-restraints excluded: chain H residue  120 SER
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 5 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3467 r_free = 0.3467 target = 0.073265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.050713 restraints weight = 35534.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.55
r_work: 0.2731 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8957
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13675  Z= 0.202
  Angle     :  0.583  10.977  19721  Z= 0.346
  Chirality :  0.036   0.200   2229
  Planarity :  0.004   0.039   1477
  Dihedral  : 30.701 178.325   4163
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.34 %
    Favored  : 77.56 %
  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:  2.49 (0.29), residues: 831
  helix:  2.71 (0.22), residues: 557
  sheet: -1.79 (0.90), residues: 23
  loop : -0.50 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  82 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.006   0.000   ARG K   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  785)
  hydrogen bonds       : angle       2.72082 ( 1960)
  covalent geometry    : bond        0.00458 (13673)
  covalent geometry    : angle       0.58317 (19721)
  Misc. bond           : bond        0.00024 (    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
  140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8607 (tm-30)
REVERT: E  120 MET cc_start: 0.9242 (mtt) cc_final: 0.8981 (mtt)
REVERT: F   20 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6569 (mmmt)
REVERT: G   73 ASN cc_start: 0.8984 (t0) cc_final: 0.8597 (t0)
REVERT: H   90 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8146 (mp0)
REVERT: K   58 ILE cc_start: 0.5777 (OUTLIER) cc_final: 0.5463 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 132
  average time/residue: 1.7480
  time to fit residues: 245.1895
Evaluate side-chains
  130 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
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 G residue   95 LYS
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.3980
   chunk 103 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    2.0788

-------------------------------------------------------------------------------
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
** 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 = 0.3420 r_free = 0.3420 target = 0.071419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.048534 restraints weight = 36192.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.58
r_work: 0.2658 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2541 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  13675  Z= 0.286
  Angle     :  0.637  10.333  19721  Z= 0.374
  Chirality :  0.040   0.148   2229
  Planarity :  0.005   0.040   1477
  Dihedral  : 30.848 177.575   4163
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.90 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.18 (0.28), residues: 831
  helix:  2.51 (0.21), residues: 555
  sheet: -2.25 (0.85), residues: 25
  loop : -0.63 (0.34), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K  82 
 HIS   0.003   0.001   HIS K  20 
 PHE   0.017   0.002   PHE K   5 
 TYR   0.015   0.002   TYR K  61 
 ARG   0.006   0.001   ARG K   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05270 (  785)
  hydrogen bonds       : angle       2.88987 ( 1960)
  covalent geometry    : bond        0.00657 (13673)
  covalent geometry    : angle       0.63731 (19721)
  Misc. bond           : bond        0.00059 (    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
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8633 (tm-30)
REVERT: E  120 MET cc_start: 0.9231 (mtt) cc_final: 0.8976 (mtt)
REVERT: F   20 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6584 (mmmt)
REVERT: G   73 ASN cc_start: 0.9066 (t0) cc_final: 0.8611 (t0)
REVERT: H   83 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8615 (mmm-85)
REVERT: K   74 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8229 (tpp80)
  outliers start: 17
  outliers final: 8
  residues processed: 129
  average time/residue: 1.7674
  time to fit residues: 242.0806
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  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   58 ILE
Chi-restraints excluded: chain K residue   74 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   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  44 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 = 0.3438 r_free = 0.3438 target = 0.072264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.049549 restraints weight = 35598.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.56
r_work: 0.2685 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8986
moved from start:          0.3532

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= 0.171
  Angle     :  0.606  11.647  19721  Z= 0.358
  Chirality :  0.036   0.124   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.845 177.718   4163
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 22.16 %
    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 (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:  2.33 (0.29), residues: 831
  helix:  2.60 (0.22), residues: 555
  sheet: -2.17 (0.86), residues: 25
  loop : -0.53 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP K  82 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.012   0.001   PHE K   5 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.005   0.000   ARG K  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04679 (  785)
  hydrogen bonds       : angle       2.80477 ( 1960)
  covalent geometry    : bond        0.00377 (13673)
  covalent geometry    : angle       0.60644 (19721)
  Misc. bond           : bond        0.00032 (    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
  134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   31 LYS cc_start: 0.8632 (mppt) cc_final: 0.8240 (mppt)
REVERT: D   68 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8635 (tm-30)
REVERT: E  120 MET cc_start: 0.9186 (mtt) cc_final: 0.8933 (mtt)
REVERT: F   20 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6634 (mmmt)
REVERT: G   73 ASN cc_start: 0.9041 (t0) cc_final: 0.8585 (t0)
REVERT: H   83 ARG cc_start: 0.8869 (mtt-85) cc_final: 0.8572 (mmm-85)
REVERT: K   58 ILE cc_start: 0.5807 (OUTLIER) cc_final: 0.5599 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 127
  average time/residue: 1.7299
  time to fit residues: 233.6739
Evaluate side-chains
  129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
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 G residue   95 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   25 VAL
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 38 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.072238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.049517 restraints weight = 35934.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.56
r_work: 0.2687 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.3700

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= 0.223
  Angle     :  0.605  10.544  19721  Z= 0.357
  Chirality :  0.037   0.123   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.633 178.475   4163
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.58 %
    Favored  : 75.32 %
  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:  2.42 (0.29), residues: 831
  helix:  2.67 (0.21), residues: 557
  sheet: -2.06 (0.86), residues: 25
  loop : -0.52 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP K  82 
 HIS   0.002   0.001   HIS F  18 
 PHE   0.012   0.001   PHE K   5 
 TYR   0.013   0.001   TYR K  61 
 ARG   0.004   0.000   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04539 (  785)
  hydrogen bonds       : angle       2.76590 ( 1960)
  covalent geometry    : bond        0.00507 (13673)
  covalent geometry    : angle       0.60510 (19721)
  Misc. bond           : bond        0.00037 (    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
  138 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   90 ASP cc_start: 0.8981 (t0) cc_final: 0.8766 (t70)
REVERT: D   68 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8643 (tm-30)
REVERT: E  120 MET cc_start: 0.9183 (mtt) cc_final: 0.8931 (mtt)
REVERT: F   20 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6597 (mmmt)
REVERT: G   73 ASN cc_start: 0.9034 (t0) cc_final: 0.8605 (t0)
REVERT: H   83 ARG cc_start: 0.8889 (mtt-85) cc_final: 0.8667 (mmt-90)
REVERT: K   58 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5785 (mt)
REVERT: K   61 TYR cc_start: 0.7300 (t80) cc_final: 0.7094 (t80)
REVERT: K   74 ARG cc_start: 0.8508 (mmt90) cc_final: 0.7830 (mtt90)
  outliers start: 15
  outliers final: 7
  residues processed: 131
  average time/residue: 1.7926
  time to fit residues: 248.8912
Evaluate side-chains
  126 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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 G residue   95 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   25 VAL
Chi-restraints excluded: chain K residue   58 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN
E  76 GLN
G 104 GLN
** K  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.072513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.049817 restraints weight = 35945.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.56
r_work: 0.2696 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2579 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8970
moved from start:          0.3691

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= 0.193
  Angle     :  0.602  11.699  19721  Z= 0.355
  Chirality :  0.036   0.123   2229
  Planarity :  0.004   0.041   1477
  Dihedral  : 30.639 178.446   4163
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 22.72 %
    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 (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:  2.46 (0.29), residues: 831
  helix:  2.68 (0.21), residues: 557
  sheet: -1.90 (0.88), residues: 25
  loop : -0.45 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K  82 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.011   0.001   PHE K   5 
 TYR   0.014   0.001   TYR K  61 
 ARG   0.004   0.000   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (  785)
  hydrogen bonds       : angle       2.74460 ( 1960)
  covalent geometry    : bond        0.00434 (13673)
  covalent geometry    : angle       0.60237 (19721)
  Misc. bond           : bond        0.00015 (    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
  130 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   68 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8624 (tm-30)
REVERT: E  120 MET cc_start: 0.9203 (mtt) cc_final: 0.8945 (mtt)
REVERT: F   20 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6609 (mmmt)
REVERT: G   73 ASN cc_start: 0.9059 (t0) cc_final: 0.8612 (t0)
REVERT: H   83 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.8647 (mmt-90)
REVERT: K   58 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5792 (mt)
REVERT: K   74 ARG cc_start: 0.8527 (mmt90) cc_final: 0.7783 (mtt90)
  outliers start: 11
  outliers final: 5
  residues processed: 125
  average time/residue: 1.7824
  time to fit residues: 236.7398
Evaluate side-chains
  124 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   25 VAL
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 67 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0170
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
E  76 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.072767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.050136 restraints weight = 35847.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 1.55
r_work: 0.2706 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2590 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  13675  Z= 0.168
  Angle     :  0.604  11.675  19721  Z= 0.355
  Chirality :  0.035   0.123   2229
  Planarity :  0.005   0.081   1477
  Dihedral  : 30.638 178.483   4163
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 23.14 %
    Favored  : 75.32 %
  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:  2.56 (0.29), residues: 831
  helix:  2.75 (0.21), residues: 557
  sheet: -1.95 (0.87), residues: 25
  loop : -0.40 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP K  21 
 HIS   0.003   0.001   HIS D  46 
 PHE   0.009   0.001   PHE K   5 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.003   0.000   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  785)
  hydrogen bonds       : angle       2.72654 ( 1960)
  covalent geometry    : bond        0.00374 (13673)
  covalent geometry    : angle       0.60436 (19721)
  Misc. bond           : bond        0.00030 (    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
  133 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   54 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8783 (mmtm)
REVERT: D   68 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8613 (tm-30)
REVERT: E  120 MET cc_start: 0.9197 (mtt) cc_final: 0.8943 (mtt)
REVERT: F   20 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6631 (mmmt)
REVERT: G   73 ASN cc_start: 0.9046 (t0) cc_final: 0.8601 (t0)
REVERT: H   83 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8643 (mmt-90)
REVERT: K   58 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5820 (mt)
REVERT: K   74 ARG cc_start: 0.8520 (mmt90) cc_final: 0.7768 (mtt90)
  outliers start: 11
  outliers final: 4
  residues processed: 127
  average time/residue: 1.8231
  time to fit residues: 245.4033
Evaluate side-chains
  124 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   25 VAL
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 0 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 14 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.072919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.050323 restraints weight = 35534.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.55
r_work: 0.2712 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2596 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
moved from start:          0.3724

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= 0.166
  Angle     :  0.601  11.624  19721  Z= 0.353
  Chirality :  0.035   0.169   2229
  Planarity :  0.004   0.070   1477
  Dihedral  : 30.614 178.492   4163
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 23.42 %
    Favored  : 75.32 %
  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:  2.62 (0.29), residues: 831
  helix:  2.79 (0.21), residues: 557
  sheet: -1.91 (0.88), residues: 25
  loop : -0.37 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP K  82 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.008   0.001   PHE K   5 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.003   0.000   ARG G  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  785)
  hydrogen bonds       : angle       2.70175 ( 1960)
  covalent geometry    : bond        0.00368 (13673)
  covalent geometry    : angle       0.60074 (19721)
  Misc. bond           : bond        0.00026 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10168.18 seconds
wall clock time: 175 minutes 37.95 seconds (10537.95 seconds total)