Starting phenix.real_space_refine
on Mon Jul 28 15:58:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b6d_12052/07_2025/7b6d_12052_neut.cif"
  }
  resolution = 4.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    6713      2.51       5
     N    1749      2.21       5
     O    1958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1337
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 7, 'TRANS': 157}
    Chain: "B"
      Number of atoms: 1226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1226
          Classifications: {'peptide': 151}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 147}
    Chain: "C"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1204
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 138}
    Chain: "D"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1741
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 1177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1177
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
    Chain: "F"
      Number of atoms: 1333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1333
          Classifications: {'peptide': 164}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 159}
    Chain: "G"
      Number of atoms: 1363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1363
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 7, 'TRANS': 161}
    Chain: "H"
      Number of atoms: 1089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1089
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
  Time building chain proxies: 7.06, per 1000 atoms: 0.67
  Number of scatterers: 10470
  At special positions: 0
  Unit cell: (167.232, 152.256, 79.872, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1958      8.00
     N    1749      7.00
     C    6713      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: 2.64
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2466

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      43.3% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 33
      removed outlier: 3.567A  pdb=" N   GLY A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 63
      removed outlier: 4.204A  pdb=" N   LEU A  43 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU A  56 " --> pdb=" O   MET A  52 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASP A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 84
    Processing helix  chain 'A' and resid 126 through 140
      removed outlier: 4.521A  pdb=" N   ALA A 136 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
    Processing helix  chain 'B' and resid 4 through 17
    Processing helix  chain 'B' and resid 27 through 42
      removed outlier: 4.352A  pdb=" N   GLU B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 70
    Processing helix  chain 'B' and resid 94 through 99
    Processing helix  chain 'B' and resid 107 through 114
      removed outlier: 3.814A  pdb=" N   LYS B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 117
      No H-bonds generated for 'chain 'B' and resid 115 through 117'
    Processing helix  chain 'C' and resid 30 through 53
    Processing helix  chain 'C' and resid 93 through 104
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 123 through 135
    Processing helix  chain 'D' and resid 81 through 88
      removed outlier: 3.635A  pdb=" N   ALA D  88 " --> pdb=" O   THR D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
      Proline residue:  D 117  - end of helix
    Processing helix  chain 'D' and resid 165 through 182
      removed outlier: 3.810A  pdb=" N   LEU D 169 " --> pdb=" O   GLY D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 210
    Processing helix  chain 'E' and resid 26 through 55
      removed outlier: 3.634A  pdb=" N   ASP E  32 " --> pdb=" O   LEU E  28 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLU E  50 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 111
    Processing helix  chain 'E' and resid 122 through 136
    Processing helix  chain 'F' and resid 32 through 50
    Processing helix  chain 'F' and resid 52 through 81
      removed outlier: 3.573A  pdb=" N   LEU F  56 " --> pdb=" O   THR F  52 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ARG F  70 " --> pdb=" O   ASP F  66 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   ASP F  73 " --> pdb=" O   THR F  69 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL F  77 " --> pdb=" O   ASP F  73 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG F  78 " --> pdb=" O   LEU F  74 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 104
      removed outlier: 3.898A  pdb=" N   TRP F 100 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 128 through 133
      removed outlier: 4.285A  pdb=" N   PHE F 133 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 144 through 160
      removed outlier: 3.691A  pdb=" N   PHE F 148 " --> pdb=" O   ASN F 144 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 181 through 192
    Processing helix  chain 'G' and resid 14 through 33
    Processing helix  chain 'G' and resid 35 through 59
      removed outlier: 3.703A  pdb=" N   VAL G  39 " --> pdb=" O   ASN G  35 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG G  53 " --> pdb=" O   ASN G  49 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE G  55 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU G  56 " --> pdb=" O   MET G  52 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP G  57 " --> pdb=" O   ARG G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 69 through 85
      removed outlier: 3.579A  pdb=" N   PHE G  81 " --> pdb=" O   ILE G  77 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG G  82 " --> pdb=" O   GLN G  78 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 117 through 121
      removed outlier: 3.539A  pdb=" N   THR G 121 " --> pdb=" O   PRO G 118 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 126 through 140
      removed outlier: 3.940A  pdb=" N   SER G 130 " --> pdb=" O   SER G 126 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ARG G 134 " --> pdb=" O   SER G 130 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL G 140 " --> pdb=" O   ALA G 136 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 48
    Processing helix  chain 'H' and resid 92 through 111
    Processing helix  chain 'H' and resid 123 through 138
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92
      removed outlier: 4.223A  pdb=" N   PHE A 101 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 163 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   GLU A 160 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLU A 143 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 80
      removed outlier: 4.172A  pdb=" N   TYR B  86 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20
      removed outlier: 6.129A  pdb=" N   LEU C  62 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS D 154 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY D   5 " --> pdb=" O   ILE D 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32
    Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 43
      removed outlier: 3.500A  pdb=" N   ASP D  41 " --> pdb=" O   SER D  48 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER D  48 " --> pdb=" O   ASP D  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66
      removed outlier: 3.616A  pdb=" N   VAL D  66 " --> pdb=" O   MET D  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 15 through 21
      removed outlier: 4.233A  pdb=" N   TYR E  17 " --> pdb=" O   ILE E   8 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR E   4 " --> pdb=" O   PHE E  21 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 110 through 113
    Processing sheet with id=AA9, first strand: chain 'G' and resid 90 through 92
      removed outlier: 7.053A  pdb=" N   GLU G 160 " --> pdb=" O   VAL G 149 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 15 through 20
      removed outlier: 3.740A  pdb=" N   LEU H  15 " --> pdb=" O   VAL H   7 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ALA H   2 " --> pdb=" O   ASP H  84 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP H  84 " --> pdb=" O   ALA H   2 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS H   4 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   VAL H  82 " --> pdb=" O   CYS H   4 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL H  77 " --> pdb=" O   THR H  73 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL H  81 " --> pdb=" O   TYR H  69 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS H  67 " --> pdb=" O   ILE H  83 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   HIS H  66 " --> pdb=" O   THR H  63 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   TYR H  61 " --> pdb=" O   ILE H  68 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   GLY H  70 " --> pdb=" O   LEU H  59 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU H  59 " --> pdb=" O   GLY H  70 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL H  72 " --> pdb=" O   LEU H  57 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   LEU H  57 " --> pdb=" O   VAL H  72 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.17

  Time building geometry restraints manager: 3.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3391
        1.34 -     1.46: 2413
        1.46 -     1.58: 4798
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 10683
  Sorted by residual:
  bond pdb=" N   GLY H  48 "
       pdb=" CA  GLY H  48 "
    ideal  model  delta    sigma   weight residual
    1.449  1.504 -0.055 1.45e-02 4.76e+03 1.44e+01
  bond pdb=" C   GLY H  48 "
       pdb=" O   GLY H  48 "
    ideal  model  delta    sigma   weight residual
    1.235  1.281 -0.046 1.35e-02 5.49e+03 1.16e+01
  bond pdb=" C   TYR H  30 "
       pdb=" O   TYR H  30 "
    ideal  model  delta    sigma   weight residual
    1.235  1.275 -0.039 1.26e-02 6.30e+03 9.74e+00
  bond pdb=" N   VAL H  39 "
       pdb=" CA  VAL H  39 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 7.94e+00
  bond pdb=" C   CYS H  43 "
       pdb=" O   CYS H  43 "
    ideal  model  delta    sigma   weight residual
    1.237  1.269 -0.033 1.17e-02 7.31e+03 7.78e+00
  ... (remaining 10678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 14038
        2.28 -     4.56: 369
        4.56 -     6.84: 37
        6.84 -     9.11: 5
        9.11 -    11.39: 1
  Bond angle restraints: 14450
  Sorted by residual:
  angle pdb=" CA  LYS H  47 "
        pdb=" C   LYS H  47 "
        pdb=" O   LYS H  47 "
      ideal   model   delta    sigma   weight residual
     120.42  115.36    5.06 1.06e+00 8.90e-01 2.28e+01
  angle pdb=" C   GLU F 109 "
        pdb=" N   LYS F 110 "
        pdb=" CA  LYS F 110 "
      ideal   model   delta    sigma   weight residual
     122.37  114.56    7.81 1.72e+00 3.38e-01 2.06e+01
  angle pdb=" N   LYS H  47 "
        pdb=" CA  LYS H  47 "
        pdb=" C   LYS H  47 "
      ideal   model   delta    sigma   weight residual
     111.36  116.29   -4.93 1.09e+00 8.42e-01 2.05e+01
  angle pdb=" CA  PRO C 138 "
        pdb=" C   PRO C 138 "
        pdb=" N   ILE C 139 "
      ideal   model   delta    sigma   weight residual
     115.95  121.01   -5.06 1.12e+00 7.97e-01 2.04e+01
  angle pdb=" C   PHE G 165 "
        pdb=" N   VAL G 166 "
        pdb=" CA  VAL G 166 "
      ideal   model   delta    sigma   weight residual
     123.08  118.78    4.30 1.01e+00 9.80e-01 1.81e+01
  ... (remaining 14445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 5792
       17.84 -    35.68: 553
       35.68 -    53.52: 79
       53.52 -    71.36: 16
       71.36 -    89.20: 11
  Dihedral angle restraints: 6451
    sinusoidal: 2653
      harmonic: 3798
  Sorted by residual:
  dihedral pdb=" CA  ASN D 216 "
           pdb=" C   ASN D 216 "
           pdb=" N   ILE D 217 "
           pdb=" CA  ILE D 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -122.18  -57.82     0      5.00e+00 4.00e-02 1.34e+02
  dihedral pdb=" CA  PRO D  35 "
           pdb=" C   PRO D  35 "
           pdb=" N   LEU D  36 "
           pdb=" CA  LEU D  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -142.52  -37.48     0      5.00e+00 4.00e-02 5.62e+01
  dihedral pdb=" CA  ASP C  87 "
           pdb=" C   ASP C  87 "
           pdb=" N   THR C  88 "
           pdb=" CA  THR C  88 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.94  -28.06     0      5.00e+00 4.00e-02 3.15e+01
  ... (remaining 6448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1367
       0.068 -    0.137: 231
       0.137 -    0.205: 27
       0.205 -    0.274: 4
       0.274 -    0.342: 2
  Chirality restraints: 1631
  Sorted by residual:
  chirality pdb=" CA  LYS H  47 "
            pdb=" N   LYS H  47 "
            pdb=" C   LYS H  47 "
            pdb=" CB  LYS H  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CB  ILE F 123 "
            pdb=" CA  ILE F 123 "
            pdb=" CG1 ILE F 123 "
            pdb=" CG2 ILE F 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CB  ILE F  72 "
            pdb=" CA  ILE F  72 "
            pdb=" CG1 ILE F  72 "
            pdb=" CG2 ILE F  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 1628 not shown)

  Planarity restraints: 1849
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H  48 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.29e+01
        pdb=" C   GLY H  48 "    0.062 2.00e-02 2.50e+03
        pdb=" O   GLY H  48 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA H  49 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 116 "    0.054 5.00e-02 4.00e+02   8.16e-02 1.06e+01
        pdb=" N   PRO A 117 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 117 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 117 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 117 "    0.051 5.00e-02 4.00e+02   7.80e-02 9.75e+00
        pdb=" N   PRO A 118 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1846 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 216
        2.62 -     3.19: 10941
        3.19 -     3.76: 18086
        3.76 -     4.33: 25073
        4.33 -     4.90: 36828
  Nonbonded interactions: 91144
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 102 "
            pdb=" OD1 ASP F  73 "
     model   vdw
     2.049 3.040
  nonbonded pdb=" OG  SER G 102 "
            pdb=" NH1 ARG G 162 "
     model   vdw
     2.085 3.120
  nonbonded pdb=" O   GLU A  69 "
            pdb=" OG1 THR A  73 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OD1 ASP A  38 "
            pdb=" NZ  LYS A  41 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" O   TYR F  45 "
            pdb=" OG  SER F  48 "
     model   vdw
     2.161 3.040
  ... (remaining 91139 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'G' and resid 10 through 174)
}

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:             5.680
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.470
  Find NCS groups from input model:        0.260
  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:             0.000
  Load rotamer database and sin/cos tables:3.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  10683  Z= 0.249
  Angle     :  0.875  11.392  14450  Z= 0.521
  Chirality :  0.053   0.342   1631
  Planarity :  0.006   0.082   1849
  Dihedral  : 14.401  89.202   3985
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 32.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.20 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.69 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.22), residues: 1274
  helix: -0.82 (0.22), residues: 505
  sheet: -1.36 (0.35), residues: 208
  loop : -2.48 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP F 100 
 HIS   0.008   0.001   HIS B  11 
 PHE   0.032   0.003   PHE C  82 
 TYR   0.021   0.002   TYR F  75 
 ARG   0.011   0.001   ARG B  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15626 (  521)
  hydrogen bonds       : angle       7.81290 ( 1482)
  covalent geometry    : bond        0.00466 (10683)
  covalent geometry    : angle       0.87496 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8503 (mmp) cc_final: 0.8065 (mmm)
REVERT: A   50 MET cc_start: 0.8292 (tmm) cc_final: 0.7942 (tmm)
REVERT: A   70 MET cc_start: 0.8530 (tpp) cc_final: 0.8264 (tpp)
REVERT: B   68 MET cc_start: 0.8528 (mmm) cc_final: 0.8277 (mmm)
REVERT: C   56 ASP cc_start: 0.7077 (m-30) cc_final: 0.6637 (t70)
REVERT: E   18 GLU cc_start: 0.8481 (pp20) cc_final: 0.8147 (pp20)
REVERT: E   42 HIS cc_start: 0.8747 (m-70) cc_final: 0.8439 (t70)
REVERT: E   83 ILE cc_start: 0.9205 (mm) cc_final: 0.8792 (tp)
REVERT: E  110 MET cc_start: 0.8913 (mpp) cc_final: 0.8580 (mpp)
REVERT: E  130 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8449 (tm-30)
REVERT: F  124 ILE cc_start: 0.7148 (tt) cc_final: 0.6915 (tp)
REVERT: G  148 PHE cc_start: 0.8853 (m-80) cc_final: 0.8511 (m-80)
REVERT: H    1 MET cc_start: 0.0673 (mmm) cc_final: 0.0281 (tpt)
REVERT: H   16 TYR cc_start: 0.8345 (p90) cc_final: 0.7859 (p90)
REVERT: H  102 LEU cc_start: 0.9569 (tp) cc_final: 0.9341 (tt)
REVERT: H  122 THR cc_start: 0.6134 (p) cc_final: 0.5795 (t)
  outliers start: 5
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2091
  time to fit residues: 41.1693
Evaluate side-chains
  90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 52 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.1980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  42 HIS
** F  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.041227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.033484 restraints weight = 115217.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.034351 restraints weight = 87639.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.035033 restraints weight = 70608.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10683  Z= 0.164
  Angle     :  0.721   8.773  14450  Z= 0.387
  Chirality :  0.047   0.203   1631
  Planarity :  0.005   0.052   1849
  Dihedral  :  7.338  71.650   1405
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 24.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  7.63 %
    Favored  : 92.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.23), residues: 1274
  helix: -0.40 (0.22), residues: 519
  sheet: -1.47 (0.34), residues: 216
  loop : -2.29 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP F 100 
 HIS   0.009   0.001   HIS E  51 
 PHE   0.028   0.002   PHE B  35 
 TYR   0.027   0.002   TYR B  17 
 ARG   0.008   0.001   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05037 (  521)
  hydrogen bonds       : angle       6.20736 ( 1482)
  covalent geometry    : bond        0.00348 (10683)
  covalent geometry    : angle       0.72077 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 1.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8278 (mmp) cc_final: 0.8055 (mmm)
REVERT: A   70 MET cc_start: 0.8515 (tpp) cc_final: 0.8092 (tpp)
REVERT: C   41 MET cc_start: 0.8697 (mmm) cc_final: 0.8416 (mtp)
REVERT: C   56 ASP cc_start: 0.7454 (m-30) cc_final: 0.6873 (t70)
REVERT: E   18 GLU cc_start: 0.8397 (pp20) cc_final: 0.8162 (pp20)
REVERT: E   42 HIS cc_start: 0.8651 (m90) cc_final: 0.8384 (m170)
REVERT: E   81 ARG cc_start: 0.8022 (mpt-90) cc_final: 0.7805 (mpt-90)
REVERT: E   83 ILE cc_start: 0.9307 (mm) cc_final: 0.8995 (tp)
REVERT: E   97 PHE cc_start: 0.8305 (t80) cc_final: 0.8022 (t80)
REVERT: E  134 ARG cc_start: 0.7558 (mpp-170) cc_final: 0.7297 (mmp80)
REVERT: E  138 LEU cc_start: 0.7323 (tp) cc_final: 0.6296 (tp)
REVERT: F  147 ASN cc_start: 0.8167 (t0) cc_final: 0.7877 (t0)
REVERT: F  177 MET cc_start: 0.8156 (tmm) cc_final: 0.7712 (tmm)
REVERT: G   43 LEU cc_start: 0.9158 (tt) cc_final: 0.8832 (pp)
REVERT: G  148 PHE cc_start: 0.8997 (m-80) cc_final: 0.8495 (m-80)
REVERT: H   16 TYR cc_start: 0.8246 (p90) cc_final: 0.7784 (p90)
REVERT: H  134 MET cc_start: 0.6443 (tpt) cc_final: 0.5635 (tpp)
  outliers start: 4
  outliers final: 3
  residues processed: 130
  average time/residue: 0.2396
  time to fit residues: 44.5441
Evaluate side-chains
  88 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 115 optimal weight:    0.3980
   chunk 95 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  77 ASN
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 216 ASN
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.041217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.033472 restraints weight = 115809.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.034342 restraints weight = 88265.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.035006 restraints weight = 70958.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10683  Z= 0.168
  Angle     :  0.711   9.139  14450  Z= 0.383
  Chirality :  0.046   0.235   1631
  Planarity :  0.005   0.042   1849
  Dihedral  :  7.138  72.855   1405
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 24.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.23 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -1.93 (0.23), residues: 1274
  helix: -0.20 (0.22), residues: 517
  sheet: -1.37 (0.34), residues: 211
  loop : -2.28 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 147 
 HIS   0.014   0.002   HIS B  11 
 PHE   0.028   0.002   PHE B 112 
 TYR   0.026   0.002   TYR B  32 
 ARG   0.008   0.001   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04926 (  521)
  hydrogen bonds       : angle       5.99241 ( 1482)
  covalent geometry    : bond        0.00360 (10683)
  covalent geometry    : angle       0.71077 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.8580 (tpp) cc_final: 0.8099 (tpp)
REVERT: C   41 MET cc_start: 0.8665 (mmm) cc_final: 0.8391 (mtp)
REVERT: C   56 ASP cc_start: 0.7328 (m-30) cc_final: 0.6820 (t70)
REVERT: D   69 MET cc_start: 0.7917 (pmm) cc_final: 0.7537 (pmm)
REVERT: E    1 MET cc_start: 0.5875 (ppp) cc_final: 0.5638 (ppp)
REVERT: E   18 GLU cc_start: 0.8408 (pp20) cc_final: 0.8091 (pp20)
REVERT: E   83 ILE cc_start: 0.9331 (mm) cc_final: 0.9000 (tp)
REVERT: F  147 ASN cc_start: 0.8020 (t0) cc_final: 0.7751 (t0)
REVERT: G  105 PHE cc_start: 0.7987 (m-80) cc_final: 0.7453 (m-80)
REVERT: G  148 PHE cc_start: 0.9021 (m-80) cc_final: 0.8499 (m-10)
REVERT: H   16 TYR cc_start: 0.8300 (p90) cc_final: 0.7849 (p90)
  outliers start: 3
  outliers final: 0
  residues processed: 130
  average time/residue: 0.3395
  time to fit residues: 64.1292
Evaluate side-chains
  84 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.041455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.033716 restraints weight = 113123.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.034598 restraints weight = 86390.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.035260 restraints weight = 69469.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10683  Z= 0.148
  Angle     :  0.671   6.268  14450  Z= 0.362
  Chirality :  0.045   0.187   1631
  Planarity :  0.005   0.063   1849
  Dihedral  :  6.849  74.475   1405
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 22.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.49 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.80 (0.23), residues: 1274
  helix: -0.08 (0.22), residues: 520
  sheet: -1.28 (0.34), residues: 208
  loop : -2.25 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 147 
 HIS   0.010   0.001   HIS B  11 
 PHE   0.023   0.002   PHE B  35 
 TYR   0.034   0.002   TYR G  48 
 ARG   0.004   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04638 (  521)
  hydrogen bonds       : angle       5.72822 ( 1482)
  covalent geometry    : bond        0.00320 (10683)
  covalent geometry    : angle       0.67122 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8697 (mmm) cc_final: 0.8380 (mmm)
REVERT: A   70 MET cc_start: 0.8294 (tpp) cc_final: 0.7806 (tpp)
REVERT: C   41 MET cc_start: 0.8661 (mmm) cc_final: 0.8436 (mtp)
REVERT: E   18 GLU cc_start: 0.8405 (pp20) cc_final: 0.8196 (pp20)
REVERT: E   83 ILE cc_start: 0.9316 (mm) cc_final: 0.9003 (tp)
REVERT: E  130 GLU cc_start: 0.8909 (tp30) cc_final: 0.8498 (mt-10)
REVERT: E  134 ARG cc_start: 0.7761 (mpp-170) cc_final: 0.7040 (mmp80)
REVERT: E  138 LEU cc_start: 0.7487 (tp) cc_final: 0.7058 (tp)
REVERT: F  147 ASN cc_start: 0.7990 (t0) cc_final: 0.7771 (t0)
REVERT: F  194 LYS cc_start: 0.7749 (mptt) cc_final: 0.7502 (mmtt)
REVERT: G  105 PHE cc_start: 0.7985 (m-80) cc_final: 0.7410 (m-80)
REVERT: G  139 MET cc_start: 0.6950 (tpt) cc_final: 0.6514 (tpt)
REVERT: G  148 PHE cc_start: 0.8997 (m-80) cc_final: 0.8338 (m-10)
REVERT: H   16 TYR cc_start: 0.8279 (p90) cc_final: 0.7852 (p90)
  outliers start: 3
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2892
  time to fit residues: 51.8894
Evaluate side-chains
  86 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 67 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 ASN
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  32 GLN
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.041388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.033344 restraints weight = 108895.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.034265 restraints weight = 81807.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.034976 restraints weight = 65153.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10683  Z= 0.144
  Angle     :  0.677   8.126  14450  Z= 0.360
  Chirality :  0.046   0.244   1631
  Planarity :  0.004   0.048   1849
  Dihedral  :  6.635  74.234   1405
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 20.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.66 (0.23), residues: 1274
  helix:  0.06 (0.22), residues: 518
  sheet: -1.20 (0.35), residues: 207
  loop : -2.19 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  94 
 HIS   0.006   0.001   HIS B  11 
 PHE   0.018   0.002   PHE H  99 
 TYR   0.030   0.002   TYR B  32 
 ARG   0.006   0.001   ARG G 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04499 (  521)
  hydrogen bonds       : angle       5.54506 ( 1482)
  covalent geometry    : bond        0.00314 (10683)
  covalent geometry    : angle       0.67668 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8736 (mmm) cc_final: 0.8442 (mmm)
REVERT: A   70 MET cc_start: 0.8357 (tpp) cc_final: 0.7812 (tpp)
REVERT: C   41 MET cc_start: 0.8658 (mmm) cc_final: 0.8390 (mtp)
REVERT: E    1 MET cc_start: 0.5723 (ppp) cc_final: 0.5507 (ppp)
REVERT: E   18 GLU cc_start: 0.8394 (pp20) cc_final: 0.8187 (pp20)
REVERT: E   83 ILE cc_start: 0.9295 (mm) cc_final: 0.8980 (tp)
REVERT: E  130 GLU cc_start: 0.8895 (tp30) cc_final: 0.8546 (mt-10)
REVERT: E  134 ARG cc_start: 0.7886 (mpp-170) cc_final: 0.7139 (mmp80)
REVERT: E  138 LEU cc_start: 0.7673 (tp) cc_final: 0.7144 (tp)
REVERT: F  113 HIS cc_start: 0.8650 (p-80) cc_final: 0.8349 (p-80)
REVERT: F  147 ASN cc_start: 0.8387 (t0) cc_final: 0.8114 (t0)
REVERT: F  194 LYS cc_start: 0.7643 (mptt) cc_final: 0.7359 (mmtt)
REVERT: G  105 PHE cc_start: 0.7956 (m-80) cc_final: 0.7381 (m-80)
REVERT: G  148 PHE cc_start: 0.9009 (m-80) cc_final: 0.8350 (m-10)
REVERT: H   16 TYR cc_start: 0.8238 (p90) cc_final: 0.7796 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2704
  time to fit residues: 48.9872
Evaluate side-chains
  83 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 118 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 123 optimal weight:    0.4980
   chunk 96 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 81 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 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 = 0.3487 r_free = 0.3487 target = 0.041767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.033569 restraints weight = 109068.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.034490 restraints weight = 82459.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.035212 restraints weight = 65984.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10683  Z= 0.134
  Angle     :  0.657   7.577  14450  Z= 0.350
  Chirality :  0.045   0.220   1631
  Planarity :  0.004   0.045   1849
  Dihedral  :  6.393  68.608   1405
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.77 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.52 (0.23), residues: 1274
  helix:  0.15 (0.23), residues: 518
  sheet: -1.05 (0.35), residues: 207
  loop : -2.12 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  94 
 HIS   0.006   0.001   HIS B  11 
 PHE   0.013   0.001   PHE G 105 
 TYR   0.027   0.002   TYR B  17 
 ARG   0.007   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  521)
  hydrogen bonds       : angle       5.40426 ( 1482)
  covalent geometry    : bond        0.00289 (10683)
  covalent geometry    : angle       0.65746 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8796 (mmm) cc_final: 0.8505 (mmm)
REVERT: A   52 MET cc_start: 0.6822 (mmt) cc_final: 0.6601 (mmt)
REVERT: A   70 MET cc_start: 0.8375 (tpp) cc_final: 0.7824 (tpp)
REVERT: C   41 MET cc_start: 0.8659 (mmm) cc_final: 0.8404 (mtp)
REVERT: C   56 ASP cc_start: 0.7418 (m-30) cc_final: 0.6950 (t70)
REVERT: E    1 MET cc_start: 0.5743 (ppp) cc_final: 0.5512 (ppp)
REVERT: E   18 GLU cc_start: 0.8385 (pp20) cc_final: 0.8178 (pp20)
REVERT: E   83 ILE cc_start: 0.9278 (mm) cc_final: 0.8973 (tp)
REVERT: E  130 GLU cc_start: 0.8899 (tp30) cc_final: 0.8636 (mt-10)
REVERT: F   59 ARG cc_start: 0.9180 (mmt180) cc_final: 0.8955 (mmm-85)
REVERT: F  113 HIS cc_start: 0.8647 (p-80) cc_final: 0.8335 (p-80)
REVERT: F  147 ASN cc_start: 0.8005 (t0) cc_final: 0.7802 (t0)
REVERT: F  163 PRO cc_start: 0.7965 (Cg_exo) cc_final: 0.7765 (Cg_endo)
REVERT: G   50 MET cc_start: 0.8074 (mtt) cc_final: 0.7861 (mmm)
REVERT: G  105 PHE cc_start: 0.7924 (m-80) cc_final: 0.7414 (m-80)
REVERT: G  148 PHE cc_start: 0.9000 (m-80) cc_final: 0.8619 (m-80)
REVERT: H   16 TYR cc_start: 0.8245 (p90) cc_final: 0.7797 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2261
  time to fit residues: 40.2814
Evaluate side-chains
  87 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 121 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.041568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.033637 restraints weight = 113268.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.034497 restraints weight = 86816.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.035162 restraints weight = 70261.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10683  Z= 0.143
  Angle     :  0.672   7.116  14450  Z= 0.359
  Chirality :  0.045   0.194   1631
  Planarity :  0.004   0.047   1849
  Dihedral  :  6.363  71.743   1405
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.52 (0.23), residues: 1274
  helix:  0.14 (0.22), residues: 523
  sheet: -1.01 (0.35), residues: 209
  loop : -2.14 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  94 
 HIS   0.008   0.001   HIS B 146 
 PHE   0.016   0.002   PHE B 115 
 TYR   0.032   0.002   TYR B  32 
 ARG   0.009   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  521)
  hydrogen bonds       : angle       5.35667 ( 1482)
  covalent geometry    : bond        0.00310 (10683)
  covalent geometry    : angle       0.67213 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8850 (mmm) cc_final: 0.8479 (mmm)
REVERT: A   52 MET cc_start: 0.7004 (mmt) cc_final: 0.6789 (mmt)
REVERT: A   70 MET cc_start: 0.8365 (tpp) cc_final: 0.7841 (tpp)
REVERT: C   41 MET cc_start: 0.8567 (mmm) cc_final: 0.8321 (mtp)
REVERT: C   56 ASP cc_start: 0.7383 (m-30) cc_final: 0.6953 (t70)
REVERT: E    1 MET cc_start: 0.5792 (ppp) cc_final: 0.5552 (ppp)
REVERT: E   81 ARG cc_start: 0.7670 (mpt180) cc_final: 0.6971 (mmt180)
REVERT: E   83 ILE cc_start: 0.9280 (mm) cc_final: 0.8947 (tp)
REVERT: E  134 ARG cc_start: 0.7882 (mpp-170) cc_final: 0.7332 (mmp80)
REVERT: F   59 ARG cc_start: 0.9175 (mmt180) cc_final: 0.8941 (mmm-85)
REVERT: F  113 HIS cc_start: 0.8698 (p-80) cc_final: 0.8355 (p-80)
REVERT: F  163 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7730 (Cg_endo)
REVERT: G   68 LEU cc_start: 0.8434 (mp) cc_final: 0.8025 (tp)
REVERT: G   70 MET cc_start: 0.6850 (mmt) cc_final: 0.6559 (mmm)
REVERT: G  105 PHE cc_start: 0.7893 (m-80) cc_final: 0.7362 (m-80)
REVERT: G  139 MET cc_start: 0.7127 (tpp) cc_final: 0.6860 (tpp)
REVERT: G  148 PHE cc_start: 0.9086 (m-80) cc_final: 0.8738 (m-80)
REVERT: H   16 TYR cc_start: 0.8279 (p90) cc_final: 0.7822 (p90)
REVERT: H  124 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8210 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2555
  time to fit residues: 42.3243
Evaluate side-chains
  83 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  33 HIS
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.041326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.033593 restraints weight = 114580.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.034488 restraints weight = 86493.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.035169 restraints weight = 69160.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10683  Z= 0.148
  Angle     :  0.684   7.558  14450  Z= 0.365
  Chirality :  0.046   0.272   1631
  Planarity :  0.004   0.048   1849
  Dihedral  :  6.271  67.070   1405
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 (0.23), residues: 1274
  helix:  0.14 (0.22), residues: 522
  sheet: -0.99 (0.35), residues: 209
  loop : -2.07 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 100 
 HIS   0.006   0.001   HIS B  11 
 PHE   0.018   0.002   PHE D 186 
 TYR   0.028   0.002   TYR B  17 
 ARG   0.009   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  521)
  hydrogen bonds       : angle       5.36260 ( 1482)
  covalent geometry    : bond        0.00325 (10683)
  covalent geometry    : angle       0.68352 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8777 (mmm) cc_final: 0.8444 (mmm)
REVERT: A   70 MET cc_start: 0.8293 (tpp) cc_final: 0.7810 (tpp)
REVERT: C   41 MET cc_start: 0.8546 (mmm) cc_final: 0.8332 (mtp)
REVERT: C   56 ASP cc_start: 0.7424 (m-30) cc_final: 0.6980 (t70)
REVERT: E    1 MET cc_start: 0.5777 (ppp) cc_final: 0.5528 (ppp)
REVERT: E   18 GLU cc_start: 0.8542 (pp20) cc_final: 0.8323 (pp20)
REVERT: E   81 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7089 (mmt180)
REVERT: E   83 ILE cc_start: 0.9257 (mm) cc_final: 0.8915 (tp)
REVERT: E  134 ARG cc_start: 0.7738 (mpp-170) cc_final: 0.7464 (mmp80)
REVERT: E  138 LEU cc_start: 0.7430 (tp) cc_final: 0.7156 (tp)
REVERT: F   59 ARG cc_start: 0.9175 (mmt180) cc_final: 0.8950 (mmm-85)
REVERT: F  113 HIS cc_start: 0.8556 (p-80) cc_final: 0.8270 (p-80)
REVERT: F  163 PRO cc_start: 0.7796 (Cg_exo) cc_final: 0.7569 (Cg_endo)
REVERT: F  182 ASP cc_start: 0.9078 (t0) cc_final: 0.8806 (t0)
REVERT: G  105 PHE cc_start: 0.7744 (m-80) cc_final: 0.7281 (m-80)
REVERT: G  139 MET cc_start: 0.7155 (tpp) cc_final: 0.6908 (tpp)
REVERT: G  148 PHE cc_start: 0.9006 (m-80) cc_final: 0.8672 (m-80)
REVERT: H   16 TYR cc_start: 0.8176 (p90) cc_final: 0.7761 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2463
  time to fit residues: 40.3833
Evaluate side-chains
  82 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0030
   chunk 11 optimal weight:    0.0270
   chunk 26 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0570
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.2980
   overall best weight:    0.1566

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  32 GLN
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 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 = 0.3522 r_free = 0.3522 target = 0.042734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.034804 restraints weight = 112505.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.035721 restraints weight = 85089.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.036425 restraints weight = 68106.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  10683  Z= 0.138
  Angle     :  0.681   8.773  14450  Z= 0.363
  Chirality :  0.046   0.198   1631
  Planarity :  0.004   0.041   1849
  Dihedral  :  6.007  65.256   1405
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.28 (0.24), residues: 1274
  helix:  0.34 (0.23), residues: 517
  sheet: -0.82 (0.36), residues: 205
  loop : -2.01 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  94 
 HIS   0.005   0.001   HIS B  11 
 PHE   0.021   0.002   PHE B  35 
 TYR   0.036   0.002   TYR B  32 
 ARG   0.005   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  521)
  hydrogen bonds       : angle       5.23341 ( 1482)
  covalent geometry    : bond        0.00294 (10683)
  covalent geometry    : angle       0.68131 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8849 (mmm) cc_final: 0.8587 (mmm)
REVERT: A   70 MET cc_start: 0.8357 (tpp) cc_final: 0.7832 (tpp)
REVERT: C    1 MET cc_start: 0.6034 (mmp) cc_final: 0.5677 (mmm)
REVERT: C   31 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8090 (ttm170)
REVERT: C   41 MET cc_start: 0.8549 (mmm) cc_final: 0.8290 (mtp)
REVERT: C   56 ASP cc_start: 0.7350 (m-30) cc_final: 0.6912 (t70)
REVERT: D   69 MET cc_start: 0.7414 (pmm) cc_final: 0.7033 (pmm)
REVERT: E    1 MET cc_start: 0.6069 (ppp) cc_final: 0.5866 (ppp)
REVERT: E   81 ARG cc_start: 0.7798 (mpt180) cc_final: 0.7116 (mmt180)
REVERT: E   83 ILE cc_start: 0.9241 (mm) cc_final: 0.8969 (tp)
REVERT: F   59 ARG cc_start: 0.9188 (mmt180) cc_final: 0.8934 (mmm-85)
REVERT: F  113 HIS cc_start: 0.8601 (p-80) cc_final: 0.8291 (p-80)
REVERT: F  133 PHE cc_start: 0.6493 (p90) cc_final: 0.6081 (p90)
REVERT: F  182 ASP cc_start: 0.9109 (t0) cc_final: 0.8841 (t0)
REVERT: G  105 PHE cc_start: 0.7823 (m-80) cc_final: 0.7304 (m-80)
REVERT: G  148 PHE cc_start: 0.9059 (m-80) cc_final: 0.8172 (m-80)
REVERT: H   16 TYR cc_start: 0.8381 (p90) cc_final: 0.7972 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2226
  time to fit residues: 39.3039
Evaluate side-chains
  90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 99 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  35 HIS
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.040779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.033224 restraints weight = 117957.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.034119 restraints weight = 88935.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.034775 restraints weight = 70891.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  10683  Z= 0.179
  Angle     :  0.719   7.851  14450  Z= 0.382
  Chirality :  0.047   0.220   1631
  Planarity :  0.005   0.038   1849
  Dihedral  :  6.261  70.565   1405
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 22.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.40 (0.23), residues: 1274
  helix:  0.16 (0.22), residues: 513
  sheet: -0.92 (0.35), residues: 212
  loop : -1.97 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 100 
 HIS   0.007   0.001   HIS B  11 
 PHE   0.020   0.002   PHE C 140 
 TYR   0.029   0.002   TYR G  48 
 ARG   0.018   0.001   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04333 (  521)
  hydrogen bonds       : angle       5.42102 ( 1482)
  covalent geometry    : bond        0.00390 (10683)
  covalent geometry    : angle       0.71893 (14450)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.8749 (mmm) cc_final: 0.8482 (mmm)
REVERT: A   52 MET cc_start: 0.7263 (mmt) cc_final: 0.7026 (mmt)
REVERT: A   70 MET cc_start: 0.8041 (tpp) cc_final: 0.7675 (tpp)
REVERT: C   41 MET cc_start: 0.8604 (mmm) cc_final: 0.8381 (mtp)
REVERT: C   56 ASP cc_start: 0.7259 (m-30) cc_final: 0.6890 (t70)
REVERT: E    1 MET cc_start: 0.5602 (ppp) cc_final: 0.5332 (ppp)
REVERT: E   18 GLU cc_start: 0.8439 (pp20) cc_final: 0.8088 (pp20)
REVERT: E   83 ILE cc_start: 0.9277 (mm) cc_final: 0.8952 (tp)
REVERT: E   91 ASP cc_start: 0.8875 (p0) cc_final: 0.8637 (p0)
REVERT: E  134 ARG cc_start: 0.7639 (mpp-170) cc_final: 0.7328 (mmp80)
REVERT: E  138 LEU cc_start: 0.7475 (tp) cc_final: 0.6956 (tp)
REVERT: F   59 ARG cc_start: 0.9134 (mmt180) cc_final: 0.8880 (mmm-85)
REVERT: F  113 HIS cc_start: 0.8591 (p-80) cc_final: 0.8276 (p-80)
REVERT: F  182 ASP cc_start: 0.9154 (t0) cc_final: 0.8887 (t0)
REVERT: G  148 PHE cc_start: 0.8895 (m-80) cc_final: 0.8618 (m-80)
REVERT: H   16 TYR cc_start: 0.8238 (p90) cc_final: 0.8025 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2473
  time to fit residues: 40.2669
Evaluate side-chains
  83 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  35 HIS
** E  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  66 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.039099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.031756 restraints weight = 119309.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.032621 restraints weight = 89068.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.033274 restraints weight = 70822.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  10683  Z= 0.256
  Angle     :  0.845   8.025  14450  Z= 0.448
  Chirality :  0.050   0.317   1631
  Planarity :  0.006   0.089   1849
  Dihedral  :  7.094  68.730   1405
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 30.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.22), residues: 1274
  helix: -0.51 (0.21), residues: 519
  sheet: -1.23 (0.35), residues: 218
  loop : -2.13 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP F 100 
 HIS   0.010   0.002   HIS B  11 
 PHE   0.032   0.003   PHE G 105 
 TYR   0.033   0.003   TYR B  32 
 ARG   0.024   0.001   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  521)
  hydrogen bonds       : angle       5.86514 ( 1482)
  covalent geometry    : bond        0.00546 (10683)
  covalent geometry    : angle       0.84534 (14450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.51 seconds
wall clock time: 62 minutes 50.68 seconds (3770.68 seconds total)