Starting phenix.real_space_refine
on Tue Jul 29 19:45:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6esf_3947/07_2025/6esf_3947.cif"
  }
  resolution = 3.7
  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=   0.011
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      12      5.16       5
     C    6680      2.51       5
     N    2275      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12091
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 678
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 804
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 683
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 811
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 7.42, per 1000 atoms: 0.61
  Number of scatterers: 12091
  At special positions: 0
  Unit cell: (82.96, 121.04, 114.24, 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      12     16.00
     P     294     15.00
     O    2830      8.00
     N    2275      7.00
     C    6680      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.96
  Conformation dependent library (CDL) restraints added in 872.2 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      68.9% alpha, 2.4% beta
      142 base pairs and 246 stacking pairs defined.
    Time for finding SS restraints: 5.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.087A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.546A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.663A  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: 3.606A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.681A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.546A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.332A  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 79
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.746A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 113
      removed outlier: 3.600A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.549A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.697A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 75
      removed outlier: 3.697A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.863A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 88
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.518A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 4.309A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
      removed outlier: 3.603A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA H 107 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.061A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.677A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.780A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.766A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78

    374 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      363 hydrogen bonds
      722 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      246 stacking parallelities
  Total time for adding SS restraints: 4.29

  Time building geometry restraints manager: 3.42 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: 1923
        1.33 -     1.45: 4420
        1.45 -     1.56: 5955
        1.56 -     1.68: 586
        1.68 -     1.80: 22
  Bond restraints: 12906
  Sorted by residual:
  bond pdb=" CB  ASP A 106 "
       pdb=" CG  ASP A 106 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.37e+00
  bond pdb=" C3'  DC J   6 "
       pdb=" O3'  DC J   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.376  0.046 3.00e-02 1.11e+03 2.36e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.468 -0.046 3.00e-02 1.11e+03 2.31e+00
  bond pdb=" C1'  DT I   9 "
       pdb=" N1   DT I   9 "
    ideal  model  delta    sigma   weight residual
    1.490  1.446  0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.06e+00
  ... (remaining 12901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 17351
        1.83 -     3.66: 1211
        3.66 -     5.49: 103
        5.49 -     7.32: 22
        7.32 -     9.14: 5
  Bond angle restraints: 18692
  Sorted by residual:
  angle pdb=" C   GLN G  84 "
        pdb=" N   LEU G  85 "
        pdb=" CA  LEU G  85 "
      ideal   model   delta    sigma   weight residual
     121.58  115.18    6.40 1.95e+00 2.63e-01 1.08e+01
  angle pdb=" C3'  DG I  20 "
        pdb=" O3'  DG I  20 "
        pdb=" P    DG I  21 "
      ideal   model   delta    sigma   weight residual
     120.20  125.05   -4.85 1.50e+00 4.44e-01 1.04e+01
  angle pdb=" C   GLN C  84 "
        pdb=" N   LEU C  85 "
        pdb=" CA  LEU C  85 "
      ideal   model   delta    sigma   weight residual
     121.14  115.58    5.56 1.75e+00 3.27e-01 1.01e+01
  angle pdb=" C   ALA C  60 "
        pdb=" N   GLU C  61 "
        pdb=" CA  GLU C  61 "
      ideal   model   delta    sigma   weight residual
     121.14  115.59    5.55 1.75e+00 3.27e-01 1.01e+01
  angle pdb=" C3'  DT I -59 "
        pdb=" C2'  DT I -59 "
        pdb=" C1'  DT I -59 "
      ideal   model   delta    sigma   weight residual
     101.60   97.03    4.57 1.50e+00 4.44e-01 9.27e+00
  ... (remaining 18687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 5499
       35.90 -    71.80: 1480
       71.80 -   107.69: 27
      107.69 -   143.59: 1
      143.59 -   179.49: 1
  Dihedral angle restraints: 7008
    sinusoidal: 4794
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  LEU E  60 "
           pdb=" C   LEU E  60 "
           pdb=" N   LEU E  61 "
           pdb=" CA  LEU E  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.84  -24.16     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  TYR H  34 "
           pdb=" C   TYR H  34 "
           pdb=" N   ALA H  35 "
           pdb=" CA  ALA H  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.97  -24.03     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  ILE A  62 "
           pdb=" C   ILE A  62 "
           pdb=" N   ARG A  63 "
           pdb=" CA  ARG A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.16  -23.84     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 7005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1518
       0.053 -    0.106: 514
       0.106 -    0.158: 90
       0.158 -    0.211: 7
       0.211 -    0.264: 1
  Chirality restraints: 2130
  Sorted by residual:
  chirality pdb=" CG  LEU G  34 "
            pdb=" CB  LEU G  34 "
            pdb=" CD1 LEU G  34 "
            pdb=" CD2 LEU G  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CG  LEU C  34 "
            pdb=" CB  LEU C  34 "
            pdb=" CD1 LEU C  34 "
            pdb=" CD2 LEU C  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  ILE D  51 "
            pdb=" CA  ILE D  51 "
            pdb=" CG1 ILE D  51 "
            pdb=" CG2 ILE D  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2127 not shown)

  Planarity restraints: 1345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  99 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.42e+00
        pdb=" N   PRO D 100 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D 100 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 100 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  67 "    0.033 2.00e-02 2.50e+03   1.59e-02 6.32e+00
        pdb=" N1   DT I  67 "   -0.034 2.00e-02 2.50e+03
        pdb=" C2   DT I  67 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2   DT I  67 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DT I  67 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I  67 "    0.009 2.00e-02 2.50e+03
        pdb=" O4   DT I  67 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DT I  67 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT I  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DT I  67 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  26 "   -0.035 2.00e-02 2.50e+03   1.46e-02 5.86e+00
        pdb=" N9   DA I  26 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I  26 "    0.017 2.00e-02 2.50e+03
        pdb=" N7   DA I  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA I  26 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6   DA I  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  26 "   -0.012 2.00e-02 2.50e+03
        pdb=" N1   DA I  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  26 "    0.011 2.00e-02 2.50e+03
        pdb=" C4   DA I  26 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1342 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2465
        2.78 -     3.31: 10427
        3.31 -     3.84: 25095
        3.84 -     4.37: 27796
        4.37 -     4.90: 38509
  Nonbonded interactions: 104292
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  73 "
            pdb=" O2   DC J -73 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE2 GLU A 133 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  68 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   VAL H 115 "
            pdb=" OG1 THR H 119 "
     model   vdw
     2.299 3.040
  ... (remaining 104287 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 37 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 38 through 134))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 18 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 119)
}
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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     32.430
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
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      :  0.008   0.070  12906  Z= 0.353
  Angle     :  0.973   9.144  18692  Z= 0.554
  Chirality :  0.052   0.264   2130
  Planarity :  0.007   0.063   1345
  Dihedral  : 28.705 179.491   5578
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  3.13 %
    Favored  : 95.92 %
  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: -4.25 (0.23), residues: 746
  helix: -2.79 (0.15), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.41 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.002   HIS B  75 
 PHE   0.033   0.004   PHE C  25 
 TYR   0.016   0.003   TYR C  50 
 ARG   0.009   0.001   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10461 (  737)
  hydrogen bonds       : angle       6.86556 ( 1838)
  covalent geometry    : bond        0.00797 (12906)
  covalent geometry    : angle       0.97312 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 282
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7454 (mttm)
REVERT: A  123 ASP cc_start: 0.7701 (m-30) cc_final: 0.7458 (m-30)
REVERT: C   33 LEU cc_start: 0.8327 (mt) cc_final: 0.7741 (tp)
REVERT: C   76 THR cc_start: 0.8924 (p) cc_final: 0.8424 (t)
REVERT: D   31 LYS cc_start: 0.7801 (mttt) cc_final: 0.7414 (pttm)
REVERT: E   74 ILE cc_start: 0.8944 (mt) cc_final: 0.8636 (mt)
REVERT: E  123 ASP cc_start: 0.7765 (m-30) cc_final: 0.7222 (m-30)
REVERT: G   33 LEU cc_start: 0.8240 (mt) cc_final: 0.7815 (tp)
REVERT: G   34 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (mt)
REVERT: G   84 GLN cc_start: 0.8332 (tp40) cc_final: 0.8090 (tp-100)
REVERT: G   95 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7804 (tppt)
REVERT: H   31 LYS cc_start: 0.8535 (tptp) cc_final: 0.8096 (ttpt)
REVERT: H   48 ASP cc_start: 0.8133 (m-30) cc_final: 0.7677 (p0)
REVERT: H   90 GLU cc_start: 0.7876 (mp0) cc_final: 0.7655 (mp0)
REVERT: H  117 LYS cc_start: 0.8643 (tttm) cc_final: 0.8380 (tttt)
  outliers start: 6
  outliers final: 1
  residues processed: 286
  average time/residue: 0.2973
  time to fit residues: 112.9451
Evaluate side-chains
  168 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   51 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
C  24 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  18 HIS
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
G  38 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.095651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.080524 restraints weight = 43841.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.082291 restraints weight = 22321.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.083480 restraints weight = 14460.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12906  Z= 0.170
  Angle     :  0.655  11.374  18692  Z= 0.382
  Chirality :  0.037   0.173   2130
  Planarity :  0.006   0.057   1345
  Dihedral  : 32.269 178.294   4065
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 14.89 %
    Favored  : 81.50 %
  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: -1.16 (0.28), residues: 746
  helix: -0.20 (0.20), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.99 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS H  46 
 PHE   0.011   0.001   PHE D  67 
 TYR   0.027   0.002   TYR B  88 
 ARG   0.008   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 (  737)
  hydrogen bonds       : angle       3.60876 ( 1838)
  covalent geometry    : bond        0.00361 (12906)
  covalent geometry    : angle       0.65499 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7983 (mm) cc_final: 0.7664 (mm)
REVERT: A   94 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7635 (mm-30)
REVERT: A  123 ASP cc_start: 0.7815 (m-30) cc_final: 0.7447 (m-30)
REVERT: C   25 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8641 (m-80)
REVERT: C   33 LEU cc_start: 0.8042 (mt) cc_final: 0.7789 (tp)
REVERT: C   64 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7355 (tm-30)
REVERT: C   76 THR cc_start: 0.8906 (p) cc_final: 0.8527 (t)
REVERT: C   85 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7389 (mt)
REVERT: C  100 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8710 (m)
REVERT: D   31 LYS cc_start: 0.7644 (mttt) cc_final: 0.7190 (pttt)
REVERT: D  117 LYS cc_start: 0.8229 (tttt) cc_final: 0.8020 (tttt)
REVERT: E  123 ASP cc_start: 0.8041 (m-30) cc_final: 0.7199 (m-30)
REVERT: F   86 VAL cc_start: 0.8792 (m) cc_final: 0.8591 (t)
REVERT: G   33 LEU cc_start: 0.8031 (mt) cc_final: 0.7814 (tp)
REVERT: G   57 TYR cc_start: 0.8706 (t80) cc_final: 0.8506 (t80)
REVERT: G   64 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: G   68 ASN cc_start: 0.8472 (t0) cc_final: 0.7760 (t0)
REVERT: H   31 LYS cc_start: 0.8193 (tptp) cc_final: 0.7811 (ttpt)
REVERT: H   39 TYR cc_start: 0.7464 (t80) cc_final: 0.6921 (t80)
REVERT: H  110 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7743 (mm-30)
REVERT: H  117 LYS cc_start: 0.8472 (tttm) cc_final: 0.8166 (ttpt)
  outliers start: 23
  outliers final: 14
  residues processed: 229
  average time/residue: 0.2311
  time to fit residues: 75.8594
Evaluate side-chains
  182 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 165
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0070
   chunk 40 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    3.2006

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.093560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.077888 restraints weight = 44143.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.079579 restraints weight = 23054.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.080697 restraints weight = 15342.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  12906  Z= 0.236
  Angle     :  0.689   8.463  18692  Z= 0.398
  Chirality :  0.038   0.160   2130
  Planarity :  0.006   0.054   1345
  Dihedral  : 32.157 179.879   4065
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 17.24 %
    Favored  : 76.33 %
  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:  0.06 (0.30), residues: 746
  helix:  0.81 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.81 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS F  75 
 PHE   0.012   0.002   PHE D  67 
 TYR   0.013   0.002   TYR C  39 
 ARG   0.007   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05520 (  737)
  hydrogen bonds       : angle       3.49260 ( 1838)
  covalent geometry    : bond        0.00523 (12906)
  covalent geometry    : angle       0.68946 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 159
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7876 (mm-30)
REVERT: A  106 ASP cc_start: 0.7043 (t70) cc_final: 0.6818 (t70)
REVERT: A  108 ASN cc_start: 0.8302 (t0) cc_final: 0.8063 (t0)
REVERT: A  123 ASP cc_start: 0.7859 (m-30) cc_final: 0.7606 (m-30)
REVERT: B   49 LEU cc_start: 0.8550 (mp) cc_final: 0.8305 (mp)
REVERT: B   74 GLU cc_start: 0.8047 (tp30) cc_final: 0.7360 (tp30)
REVERT: C   33 LEU cc_start: 0.8407 (mt) cc_final: 0.8060 (tp)
REVERT: C   64 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7472 (tm-30)
REVERT: C   76 THR cc_start: 0.8939 (p) cc_final: 0.8686 (t)
REVERT: D   31 LYS cc_start: 0.7725 (mttt) cc_final: 0.7339 (pttt)
REVERT: D   59 MET cc_start: 0.8365 (tpp) cc_final: 0.7735 (tpp)
REVERT: E  123 ASP cc_start: 0.8097 (m-30) cc_final: 0.7508 (m-30)
REVERT: G   33 LEU cc_start: 0.8206 (mt) cc_final: 0.7858 (tp)
REVERT: G   61 GLU cc_start: 0.8049 (tp30) cc_final: 0.7828 (tp30)
REVERT: G   68 ASN cc_start: 0.8701 (t0) cc_final: 0.8055 (t0)
REVERT: H   31 LYS cc_start: 0.8233 (tptp) cc_final: 0.7720 (ttpt)
REVERT: H   48 ASP cc_start: 0.7697 (p0) cc_final: 0.7308 (p0)
REVERT: H  102 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6500 (tm-30)
REVERT: H  110 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7585 (mm-30)
  outliers start: 41
  outliers final: 33
  residues processed: 191
  average time/residue: 0.2098
  time to fit residues: 59.4575
Evaluate side-chains
  182 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0010
   chunk 19 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.081125 restraints weight = 43196.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.082861 restraints weight = 22471.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.084013 restraints weight = 14914.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12906  Z= 0.155
  Angle     :  0.603   9.601  18692  Z= 0.350
  Chirality :  0.035   0.165   2130
  Planarity :  0.005   0.055   1345
  Dihedral  : 31.871 177.799   4065
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.12 %
    Favored  : 76.49 %
  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:  0.82 (0.31), residues: 746
  helix:  1.42 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.66 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.010   0.001   TYR G  57 
 ARG   0.004   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04298 (  737)
  hydrogen bonds       : angle       3.03975 ( 1838)
  covalent geometry    : bond        0.00333 (12906)
  covalent geometry    : angle       0.60293 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8039 (p) cc_final: 0.7784 (p)
REVERT: A  123 ASP cc_start: 0.7908 (m-30) cc_final: 0.7515 (m-30)
REVERT: B   74 GLU cc_start: 0.8122 (tp30) cc_final: 0.7393 (tp30)
REVERT: C   33 LEU cc_start: 0.8230 (mt) cc_final: 0.7944 (tp)
REVERT: C   56 GLU cc_start: 0.8189 (tt0) cc_final: 0.7602 (tm-30)
REVERT: C   64 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: C   76 THR cc_start: 0.8832 (p) cc_final: 0.8548 (t)
REVERT: C  100 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8620 (m)
REVERT: D   31 LYS cc_start: 0.7363 (mttt) cc_final: 0.7078 (pttt)
REVERT: D   59 MET cc_start: 0.8250 (tpp) cc_final: 0.7635 (tpp)
REVERT: D  117 LYS cc_start: 0.8129 (tttt) cc_final: 0.7682 (ttpt)
REVERT: E   82 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8362 (mt)
REVERT: E  123 ASP cc_start: 0.8050 (m-30) cc_final: 0.7485 (m-30)
REVERT: G   61 GLU cc_start: 0.7754 (tp30) cc_final: 0.7507 (tp30)
REVERT: G   64 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: G   68 ASN cc_start: 0.8638 (t0) cc_final: 0.7745 (t0)
REVERT: G  100 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8680 (m)
REVERT: H   31 LYS cc_start: 0.8103 (tptp) cc_final: 0.7624 (ttpt)
REVERT: H   34 TYR cc_start: 0.8413 (m-80) cc_final: 0.8081 (m-10)
REVERT: H   43 LYS cc_start: 0.8370 (mttt) cc_final: 0.8120 (mptt)
REVERT: H   48 ASP cc_start: 0.7740 (p0) cc_final: 0.7285 (p0)
REVERT: H  102 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6383 (tm-30)
REVERT: H  110 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7692 (mm-30)
REVERT: H  117 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8013 (ttpt)
  outliers start: 28
  outliers final: 19
  residues processed: 199
  average time/residue: 0.2163
  time to fit residues: 62.7962
Evaluate side-chains
  174 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0670
   chunk 55 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.5522

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 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 = 0.3759 r_free = 0.3759 target = 0.096077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.080329 restraints weight = 43179.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.082017 restraints weight = 22746.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.083138 restraints weight = 15189.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12906  Z= 0.166
  Angle     :  0.611   9.165  18692  Z= 0.351
  Chirality :  0.035   0.162   2130
  Planarity :  0.005   0.055   1345
  Dihedral  : 31.731 178.201   4063
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.53 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.31), residues: 746
  helix:  1.66 (0.22), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.48 (0.44), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.007   0.001   PHE H  67 
 TYR   0.012   0.001   TYR B  88 
 ARG   0.004   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04400 (  737)
  hydrogen bonds       : angle       3.01056 ( 1838)
  covalent geometry    : bond        0.00364 (12906)
  covalent geometry    : angle       0.61073 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7373 (m-80) cc_final: 0.6757 (m-80)
REVERT: A   87 SER cc_start: 0.8108 (p) cc_final: 0.7785 (p)
REVERT: A  123 ASP cc_start: 0.7801 (m-30) cc_final: 0.6992 (m-30)
REVERT: B   88 TYR cc_start: 0.6475 (m-10) cc_final: 0.6265 (m-80)
REVERT: C   33 LEU cc_start: 0.8348 (mt) cc_final: 0.8033 (tp)
REVERT: C   64 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: C   76 THR cc_start: 0.8804 (p) cc_final: 0.8593 (t)
REVERT: C  100 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8672 (m)
REVERT: D   31 LYS cc_start: 0.7395 (mttt) cc_final: 0.7110 (pttt)
REVERT: D   59 MET cc_start: 0.8308 (tpp) cc_final: 0.7642 (tpp)
REVERT: D  117 LYS cc_start: 0.8177 (tttt) cc_final: 0.7816 (ttmt)
REVERT: E   50 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7498 (mm-30)
REVERT: E   82 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: E  123 ASP cc_start: 0.8177 (m-30) cc_final: 0.7472 (m-30)
REVERT: G   61 GLU cc_start: 0.7807 (tp30) cc_final: 0.7540 (tp30)
REVERT: G   68 ASN cc_start: 0.8558 (t0) cc_final: 0.7748 (t0)
REVERT: H   31 LYS cc_start: 0.8075 (tptp) cc_final: 0.7615 (ttpt)
REVERT: H   34 TYR cc_start: 0.8424 (m-80) cc_final: 0.8047 (m-10)
REVERT: H   39 TYR cc_start: 0.7533 (t80) cc_final: 0.7254 (t80)
REVERT: H   48 ASP cc_start: 0.7820 (p0) cc_final: 0.7299 (p0)
REVERT: H  110 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7641 (mm-30)
REVERT: H  117 LYS cc_start: 0.8434 (ttpt) cc_final: 0.7980 (ttpt)
  outliers start: 33
  outliers final: 21
  residues processed: 181
  average time/residue: 0.1963
  time to fit residues: 53.2568
Evaluate side-chains
  170 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
H 106 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.097388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.081610 restraints weight = 43946.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.083347 restraints weight = 22942.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.084504 restraints weight = 15216.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12906  Z= 0.149
  Angle     :  0.604   9.669  18692  Z= 0.343
  Chirality :  0.034   0.158   2130
  Planarity :  0.004   0.056   1345
  Dihedral  : 31.610 177.909   4063
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.20 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.47 (0.31), residues: 746
  helix:  1.89 (0.22), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.32 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.010   0.001   PHE H  67 
 TYR   0.012   0.001   TYR H  39 
 ARG   0.003   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  737)
  hydrogen bonds       : angle       2.89658 ( 1838)
  covalent geometry    : bond        0.00322 (12906)
  covalent geometry    : angle       0.60435 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7370 (m-80) cc_final: 0.6802 (m-80)
REVERT: A   87 SER cc_start: 0.8085 (p) cc_final: 0.7869 (p)
REVERT: A  123 ASP cc_start: 0.7791 (m-30) cc_final: 0.7060 (m-30)
REVERT: C   33 LEU cc_start: 0.8293 (mt) cc_final: 0.8012 (tp)
REVERT: C   56 GLU cc_start: 0.8077 (tt0) cc_final: 0.7414 (tm-30)
REVERT: C   64 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7404 (tm-30)
REVERT: C   76 THR cc_start: 0.8782 (p) cc_final: 0.8573 (t)
REVERT: C  100 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8653 (m)
REVERT: D   59 MET cc_start: 0.8217 (tpp) cc_final: 0.7558 (tpp)
REVERT: D   90 GLU cc_start: 0.8037 (mp0) cc_final: 0.7750 (pm20)
REVERT: D  117 LYS cc_start: 0.8147 (tttt) cc_final: 0.7799 (ttmt)
REVERT: E   50 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7318 (mm-30)
REVERT: E   82 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (mt)
REVERT: E  123 ASP cc_start: 0.8020 (m-30) cc_final: 0.7158 (m-30)
REVERT: G   68 ASN cc_start: 0.8390 (t0) cc_final: 0.7696 (t0)
REVERT: H   31 LYS cc_start: 0.8050 (tptp) cc_final: 0.7564 (ttpt)
REVERT: H   34 TYR cc_start: 0.8325 (m-80) cc_final: 0.7968 (m-10)
REVERT: H   48 ASP cc_start: 0.7643 (p0) cc_final: 0.7172 (p0)
REVERT: H   58 ILE cc_start: 0.9061 (tt) cc_final: 0.8846 (tt)
REVERT: H   59 MET cc_start: 0.8443 (tpp) cc_final: 0.7967 (tpp)
REVERT: H  117 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7966 (ttpt)
  outliers start: 21
  outliers final: 15
  residues processed: 182
  average time/residue: 0.2069
  time to fit residues: 56.6141
Evaluate side-chains
  168 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 58 optimal weight:    0.4980
   chunk 93 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  85 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.097765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.082017 restraints weight = 43560.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.083724 restraints weight = 22682.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.084893 restraints weight = 15013.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12906  Z= 0.149
  Angle     :  0.620  10.131  18692  Z= 0.346
  Chirality :  0.034   0.158   2130
  Planarity :  0.004   0.056   1345
  Dihedral  : 31.523 178.036   4063
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.98 %
    Favored  : 72.41 %
  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:  1.53 (0.31), residues: 746
  helix:  1.91 (0.22), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.21 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.011   0.001   PHE H  67 
 TYR   0.020   0.001   TYR B  88 
 ARG   0.003   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  737)
  hydrogen bonds       : angle       2.87640 ( 1838)
  covalent geometry    : bond        0.00324 (12906)
  covalent geometry    : angle       0.61984 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7386 (m-80) cc_final: 0.6825 (m-80)
REVERT: A   87 SER cc_start: 0.8167 (p) cc_final: 0.7909 (p)
REVERT: A  123 ASP cc_start: 0.7801 (m-30) cc_final: 0.7247 (m-30)
REVERT: C   33 LEU cc_start: 0.8336 (mt) cc_final: 0.8022 (tp)
REVERT: C   56 GLU cc_start: 0.8121 (tt0) cc_final: 0.7458 (tm-30)
REVERT: C   64 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7514 (tm-30)
REVERT: C   76 THR cc_start: 0.8665 (p) cc_final: 0.8458 (t)
REVERT: C  100 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8690 (m)
REVERT: D   59 MET cc_start: 0.8199 (tpp) cc_final: 0.7552 (tpp)
REVERT: D   90 GLU cc_start: 0.8128 (mp0) cc_final: 0.7765 (pm20)
REVERT: D  117 LYS cc_start: 0.8111 (tttt) cc_final: 0.7717 (ttpt)
REVERT: E  123 ASP cc_start: 0.7871 (m-30) cc_final: 0.7194 (m-30)
REVERT: H   31 LYS cc_start: 0.8017 (tptp) cc_final: 0.7513 (ttpt)
REVERT: H   34 TYR cc_start: 0.8342 (m-80) cc_final: 0.8014 (m-10)
REVERT: H   43 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (mptt)
REVERT: H   48 ASP cc_start: 0.7584 (p0) cc_final: 0.7102 (p0)
REVERT: H  117 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8046 (ttpt)
  outliers start: 23
  outliers final: 16
  residues processed: 182
  average time/residue: 0.2480
  time to fit residues: 66.7783
Evaluate side-chains
  174 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** 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 = 0.3758 r_free = 0.3758 target = 0.096207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.080262 restraints weight = 44358.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.081953 restraints weight = 23244.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.083102 restraints weight = 15503.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12906  Z= 0.184
  Angle     :  0.645   9.420  18692  Z= 0.362
  Chirality :  0.035   0.180   2130
  Planarity :  0.005   0.054   1345
  Dihedral  : 31.542 177.985   4063
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.14 %
    Favored  : 71.94 %
  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:  1.49 (0.31), residues: 746
  helix:  1.87 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.20 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.014   0.001   TYR B  51 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  737)
  hydrogen bonds       : angle       3.05620 ( 1838)
  covalent geometry    : bond        0.00409 (12906)
  covalent geometry    : angle       0.64509 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7680 (mttt)
REVERT: A   87 SER cc_start: 0.8153 (p) cc_final: 0.7807 (p)
REVERT: A  123 ASP cc_start: 0.7953 (m-30) cc_final: 0.7033 (m-30)
REVERT: C   33 LEU cc_start: 0.8420 (mt) cc_final: 0.8095 (tp)
REVERT: C   64 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7547 (tm-30)
REVERT: C   76 THR cc_start: 0.8705 (p) cc_final: 0.8486 (t)
REVERT: C  100 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8692 (m)
REVERT: D   59 MET cc_start: 0.8268 (tpp) cc_final: 0.7569 (tpp)
REVERT: D   90 GLU cc_start: 0.8116 (mp0) cc_final: 0.7780 (pm20)
REVERT: E  123 ASP cc_start: 0.7934 (m-30) cc_final: 0.7405 (m-30)
REVERT: H   31 LYS cc_start: 0.8233 (tptp) cc_final: 0.7701 (ttpt)
REVERT: H   34 TYR cc_start: 0.8417 (m-80) cc_final: 0.8020 (m-10)
REVERT: H   48 ASP cc_start: 0.7762 (p0) cc_final: 0.7209 (p0)
REVERT: H  110 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: H  117 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8058 (ttpt)
  outliers start: 25
  outliers final: 22
  residues processed: 176
  average time/residue: 0.2092
  time to fit residues: 54.4515
Evaluate side-chains
  170 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   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  68 GLN
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 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 = 0.3783 r_free = 0.3783 target = 0.097646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.082003 restraints weight = 43551.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.083703 restraints weight = 22672.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.084878 restraints weight = 15016.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12906  Z= 0.153
  Angle     :  0.640   9.867  18692  Z= 0.357
  Chirality :  0.035   0.173   2130
  Planarity :  0.005   0.056   1345
  Dihedral  : 31.467 177.713   4063
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.65 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.61 (0.31), residues: 746
  helix:  1.93 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.08 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.006   0.001   PHE D  67 
 TYR   0.014   0.001   TYR B  51 
 ARG   0.004   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  737)
  hydrogen bonds       : angle       2.96468 ( 1838)
  covalent geometry    : bond        0.00336 (12906)
  covalent geometry    : angle       0.64014 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7547 (m-80) cc_final: 0.6911 (m-80)
REVERT: A   87 SER cc_start: 0.8263 (p) cc_final: 0.7905 (p)
REVERT: A  123 ASP cc_start: 0.7883 (m-30) cc_final: 0.7080 (m-30)
REVERT: C   33 LEU cc_start: 0.8303 (mt) cc_final: 0.8025 (tp)
REVERT: C   56 GLU cc_start: 0.8172 (tt0) cc_final: 0.7491 (tm-30)
REVERT: C   64 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: C   76 THR cc_start: 0.8664 (p) cc_final: 0.8460 (t)
REVERT: C  100 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8701 (m)
REVERT: D   59 MET cc_start: 0.8176 (tpp) cc_final: 0.7520 (tpp)
REVERT: D   90 GLU cc_start: 0.8162 (mp0) cc_final: 0.7836 (pm20)
REVERT: D  117 LYS cc_start: 0.8119 (tttt) cc_final: 0.7740 (ttpt)
REVERT: E  123 ASP cc_start: 0.7877 (m-30) cc_final: 0.7235 (m-30)
REVERT: F   82 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8451 (p)
REVERT: F   84 MET cc_start: 0.7591 (tpp) cc_final: 0.6782 (tpp)
REVERT: F   88 TYR cc_start: 0.6942 (m-10) cc_final: 0.6129 (m-80)
REVERT: H   31 LYS cc_start: 0.8038 (tptp) cc_final: 0.7525 (ttpt)
REVERT: H   34 TYR cc_start: 0.8304 (m-80) cc_final: 0.7943 (m-10)
REVERT: H   48 ASP cc_start: 0.7741 (p0) cc_final: 0.7190 (p0)
REVERT: H  110 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: H  117 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8034 (ttpt)
  outliers start: 21
  outliers final: 13
  residues processed: 183
  average time/residue: 0.2255
  time to fit residues: 60.0932
Evaluate side-chains
  175 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.096763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.081148 restraints weight = 43810.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.082854 restraints weight = 22909.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.083974 restraints weight = 15191.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12906  Z= 0.170
  Angle     :  0.661   9.475  18692  Z= 0.367
  Chirality :  0.035   0.170   2130
  Planarity :  0.005   0.055   1345
  Dihedral  : 31.457 177.842   4061
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 26.65 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.31), residues: 746
  helix:  1.91 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.16 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B  51 
 ARG   0.006   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04293 (  737)
  hydrogen bonds       : angle       3.04874 ( 1838)
  covalent geometry    : bond        0.00378 (12906)
  covalent geometry    : angle       0.66110 (18692)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8208 (p) cc_final: 0.7843 (p)
REVERT: A  123 ASP cc_start: 0.7914 (m-30) cc_final: 0.7092 (m-30)
REVERT: B   74 GLU cc_start: 0.7897 (tp30) cc_final: 0.7663 (tp30)
REVERT: C   33 LEU cc_start: 0.8377 (mt) cc_final: 0.8061 (tp)
REVERT: C   64 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: C  100 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8686 (m)
REVERT: D   59 MET cc_start: 0.8259 (tpp) cc_final: 0.7571 (tpp)
REVERT: D   90 GLU cc_start: 0.8182 (mp0) cc_final: 0.7836 (pm20)
REVERT: E   73 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: E  123 ASP cc_start: 0.7874 (m-30) cc_final: 0.7229 (m-30)
REVERT: F   84 MET cc_start: 0.7171 (tpp) cc_final: 0.6632 (tpp)
REVERT: H   31 LYS cc_start: 0.8200 (tptp) cc_final: 0.7645 (ttpt)
REVERT: H   34 TYR cc_start: 0.8335 (m-80) cc_final: 0.7943 (m-10)
REVERT: H   48 ASP cc_start: 0.7758 (p0) cc_final: 0.7188 (p0)
REVERT: H  117 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8047 (ttpt)
  outliers start: 18
  outliers final: 15
  residues processed: 174
  average time/residue: 0.2195
  time to fit residues: 56.5626
Evaluate side-chains
  172 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 99 optimal weight:   10.0000
   chunk 17 optimal weight:    0.1980
   chunk 96 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 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 = 0.3769 r_free = 0.3769 target = 0.096821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.080774 restraints weight = 43416.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.082508 restraints weight = 22417.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.083665 restraints weight = 14707.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12906  Z= 0.178
  Angle     :  0.667   9.252  18692  Z= 0.371
  Chirality :  0.036   0.166   2130
  Planarity :  0.005   0.054   1345
  Dihedral  : 31.485 177.759   4061
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 26.96 %
    Favored  : 69.91 %
  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:  1.54 (0.31), residues: 746
  helix:  1.90 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.19 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.008   0.001   PHE D  67 
 TYR   0.018   0.002   TYR H  80 
 ARG   0.004   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04446 (  737)
  hydrogen bonds       : angle       3.15749 ( 1838)
  covalent geometry    : bond        0.00397 (12906)
  covalent geometry    : angle       0.66715 (18692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3272.95 seconds
wall clock time: 57 minutes 26.57 seconds (3446.57 seconds total)