Starting phenix.real_space_refine
on Sat Dec 28 00:00:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mc0_23752/12_2024/7mc0_23752.cif"
  }
  resolution = 3.3
  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=   0.018
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      33      5.16       5
     C    4540      2.51       5
     N    1237      2.21       5
     O    1282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7092
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1661
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 6, 'TRANS': 215}
    Chain: "B"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1661
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 6, 'TRANS': 215}
    Chain: "C"
      Number of atoms: 1872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1872
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 9, 'TRANS': 232}
    Chain: "D"
      Number of atoms: 1898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1898
          Classifications: {'peptide': 245}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 235}
  Time building chain proxies: 5.49, per 1000 atoms: 0.77
  Number of scatterers: 7092
  At special positions: 0
  Unit cell: (79.608, 92.448, 110.424, 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      33     16.00
     O    1282      8.00
     N    1237      7.00
     C    4540      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: 1.90
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      66.9% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 52
      removed outlier: 3.623A  pdb=" N   GLY A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU A  19 " --> pdb=" O   GLY A  15 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ARG A  22 " --> pdb=" O   ASP A  18 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A  29 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER A  34 " --> pdb=" O   MET A  30 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A  40 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 78 through 86
    Processing helix  chain 'A' and resid 86 through 95
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.702A  pdb=" N   VAL A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ARG A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 125 " --> pdb=" O   GLN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 137
      removed outlier: 4.007A  pdb=" N   ILE A 131 " --> pdb=" O   PRO A 127 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   MET A 137 " --> pdb=" O   ALA A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.888A  pdb=" N   CYS A 146 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 153 through 179
      removed outlier: 4.124A  pdb=" N   VAL A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   SER A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   SER A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   MET A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 191
      removed outlier: 4.272A  pdb=" N   ARG A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 226
    Processing helix  chain 'B' and resid 6 through 16
      removed outlier: 3.555A  pdb=" N   MET B  16 " --> pdb=" O   THR B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 52
      removed outlier: 3.810A  pdb=" N   VAL B  29 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU B  33 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER B  34 " --> pdb=" O   MET B  30 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   THR B  36 " --> pdb=" O   GLY B  32 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR B  43 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B  40 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 77
    Processing helix  chain 'B' and resid 78 through 86
      removed outlier: 3.595A  pdb=" N   LEU B  82 " --> pdb=" O   PRO B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 95
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 3.735A  pdb=" N   VAL B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE B 113 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 137
      removed outlier: 3.982A  pdb=" N   ILE B 131 " --> pdb=" O   PRO B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 180
      removed outlier: 3.537A  pdb=" N   VAL B 148 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   LEU B 149 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B 150 " --> pdb=" O   CYS B 146 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ALA B 155 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   GLY B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   SER B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 166 " --> pdb=" O   THR B 162 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR B 171 " --> pdb=" O   GLY B 167 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   MET B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 189
    Processing helix  chain 'B' and resid 196 through 226
      removed outlier: 3.867A  pdb=" N   PHE B 202 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 203 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP B 226 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 53
      removed outlier: 3.650A  pdb=" N   ILE C  52 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN C  53 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 73
      No H-bonds generated for 'chain 'C' and resid 71 through 73'
    Processing helix  chain 'C' and resid 74 through 84
      removed outlier: 4.165A  pdb=" N   GLN C  80 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN C  83 " --> pdb=" O   ARG C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 111
      removed outlier: 3.565A  pdb=" N   VAL C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      Proline residue:  C 107  - end of helix
    Processing helix  chain 'C' and resid 114 through 129
      removed outlier: 3.541A  pdb=" N   LYS C 123 " --> pdb=" O   LYS C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 157
      removed outlier: 3.605A  pdb=" N   ALA C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 172
      removed outlier: 4.469A  pdb=" N   ALA C 171 " --> pdb=" O   PRO C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 192
      removed outlier: 4.115A  pdb=" N   SER C 179 " --> pdb=" O   ALA C 175 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   CYS C 183 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 209
      removed outlier: 4.272A  pdb=" N   ILE C 205 " --> pdb=" O   GLU C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.767A  pdb=" N   ARG C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 53
      removed outlier: 3.826A  pdb=" N   ASN D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 74
      removed outlier: 4.192A  pdb=" N   ASP D  74 " --> pdb=" O   LEU D  70 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 70 through 74'
    Processing helix  chain 'D' and resid 77 through 82
    Processing helix  chain 'D' and resid 99 through 112
      Proline residue:  D 107  - end of helix
    Processing helix  chain 'D' and resid 114 through 128
    Processing helix  chain 'D' and resid 131 through 135
      removed outlier: 3.673A  pdb=" N   ALA D 135 " --> pdb=" O   THR D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 142
      removed outlier: 3.722A  pdb=" N   LEU D 142 " --> pdb=" O   PRO D 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 157
    Processing helix  chain 'D' and resid 173 through 188
      removed outlier: 3.603A  pdb=" N   SER D 179 " --> pdb=" O   ALA D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 209
    Processing helix  chain 'D' and resid 235 through 243
      removed outlier: 3.929A  pdb=" N   GLU D 240 " --> pdb=" O   ASP D 236 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU D 241 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 28
      removed outlier: 6.266A  pdb=" N   VAL C   7 " --> pdb=" O   PRO C  24 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   SER C  26 " --> pdb=" O   ASP C   5 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ASP C   5 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLU C  28 " --> pdb=" O   ILE C   3 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE C   3 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LYS C  62 " --> pdb=" O   ASP C   5 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   VAL C   7 " --> pdb=" O   SER C  60 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   SER C  60 " --> pdb=" O   VAL C   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 88
      removed outlier: 6.657A  pdb=" N   ILE C 163 " --> pdb=" O   VAL C 196 " (cutoff:3.500A)
      removed outlier: 8.510A  pdb=" N   VAL C 198 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ALA C 165 " --> pdb=" O   VAL C 198 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY C  36 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU C 215 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   MET C  38 " --> pdb=" O   LEU C 215 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ALA C 212 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE C 223 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   LEU C 214 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 25
      removed outlier: 6.446A  pdb=" N   VAL D   7 " --> pdb=" O   PRO D  24 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL D   7 " --> pdb=" O   SER D  60 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   SER D  60 " --> pdb=" O   VAL D   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 36 through 38
      removed outlier: 3.581A  pdb=" N   LEU D  37 " --> pdb=" O   ILE D 197 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR D 199 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   VAL D 198 " --> pdb=" O   ILE D 163 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA D 165 " --> pdb=" O   VAL D 198 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 211 through 216
      removed outlier: 3.749A  pdb=" N   GLU D 222 " --> pdb=" O   LEU D 214 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ASP D 216 " --> pdb=" O   VAL D 220 " (cutoff:3.500A)
      removed outlier: 5.351A  pdb=" N   VAL D 220 " --> pdb=" O   ASP D 216 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1191 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: 1.84

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1233
        1.32 -     1.44: 1633
        1.44 -     1.57: 4264
        1.57 -     1.69: 2
        1.69 -     1.81: 56
  Bond restraints: 7188
  Sorted by residual:
  bond pdb=" CA  LEU D 208 "
       pdb=" C   LEU D 208 "
    ideal  model  delta    sigma   weight residual
    1.525  1.593 -0.068 1.22e-02 6.72e+03 3.12e+01
  bond pdb=" C   PRO B 140 "
       pdb=" O   PRO B 140 "
    ideal  model  delta    sigma   weight residual
    1.243  1.198  0.045 8.50e-03 1.38e+04 2.83e+01
  bond pdb=" N   LYS D 159 "
       pdb=" CA  LYS D 159 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 7.40e-03 1.83e+04 1.99e+01
  bond pdb=" N   GLU D 167 "
       pdb=" CA  GLU D 167 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.039 9.10e-03 1.21e+04 1.79e+01
  bond pdb=" CA  LEU C  54 "
       pdb=" C   LEU C  54 "
    ideal  model  delta    sigma   weight residual
    1.526  1.581 -0.055 1.35e-02 5.49e+03 1.68e+01
  ... (remaining 7183 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 8710
        2.64 -     5.27: 957
        5.27 -     7.91: 54
        7.91 -    10.54: 10
       10.54 -    13.18: 2
  Bond angle restraints: 9733
  Sorted by residual:
  angle pdb=" N   ASN C  53 "
        pdb=" CA  ASN C  53 "
        pdb=" C   ASN C  53 "
      ideal   model   delta    sigma   weight residual
     113.20  100.02   13.18 1.21e+00 6.83e-01 1.19e+02
  angle pdb=" N   LEU C  55 "
        pdb=" CA  LEU C  55 "
        pdb=" C   LEU C  55 "
      ideal   model   delta    sigma   weight residual
     111.24   99.20   12.04 1.29e+00 6.01e-01 8.71e+01
  angle pdb=" N   ARG B  75 "
        pdb=" CA  ARG B  75 "
        pdb=" C   ARG B  75 "
      ideal   model   delta    sigma   weight residual
     114.04  104.13    9.91 1.24e+00 6.50e-01 6.39e+01
  angle pdb=" N   ASP C  15 "
        pdb=" CA  ASP C  15 "
        pdb=" C   ASP C  15 "
      ideal   model   delta    sigma   weight residual
     113.41  104.43    8.98 1.22e+00 6.72e-01 5.42e+01
  angle pdb=" N   LYS D 189 "
        pdb=" CA  LYS D 189 "
        pdb=" C   LYS D 189 "
      ideal   model   delta    sigma   weight residual
     111.03  103.25    7.78 1.11e+00 8.12e-01 4.91e+01
  ... (remaining 9728 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 3982
       17.18 -    34.36: 322
       34.36 -    51.55: 54
       51.55 -    68.73: 12
       68.73 -    85.91: 2
  Dihedral angle restraints: 4372
    sinusoidal: 1711
      harmonic: 2661
  Sorted by residual:
  dihedral pdb=" C   PHE D  92 "
           pdb=" N   PHE D  92 "
           pdb=" CA  PHE D  92 "
           pdb=" CB  PHE D  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.74   12.14     0      2.50e+00 1.60e-01 2.36e+01
  dihedral pdb=" C   THR A  12 "
           pdb=" N   THR A  12 "
           pdb=" CA  THR A  12 "
           pdb=" CB  THR A  12 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.94   11.94     0      2.50e+00 1.60e-01 2.28e+01
  dihedral pdb=" CA  GLN D  91 "
           pdb=" C   GLN D  91 "
           pdb=" N   PHE D  92 "
           pdb=" CA  PHE D  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.56  -23.44     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 768
       0.089 -    0.178: 319
       0.178 -    0.267: 79
       0.267 -    0.356: 20
       0.356 -    0.445: 3
  Chirality restraints: 1189
  Sorted by residual:
  chirality pdb=" CA  THR A  12 "
            pdb=" N   THR A  12 "
            pdb=" C   THR A  12 "
            pdb=" CB  THR A  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.08    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CA  GLU C 167 "
            pdb=" N   GLU C 167 "
            pdb=" C   GLU C 167 "
            pdb=" CB  GLU C 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CA  PHE C  92 "
            pdb=" N   PHE C  92 "
            pdb=" C   PHE C  92 "
            pdb=" CB  PHE C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.33e+00
  ... (remaining 1186 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D  91 "   -0.020 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   GLN D  91 "    0.068 2.00e-02 2.50e+03
        pdb=" O   GLN D  91 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PHE D  92 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  54 "    0.019 2.00e-02 2.50e+03   3.88e-02 1.51e+01
        pdb=" C   LEU C  54 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   LEU C  54 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU C  55 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A   9 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   ALA A   9 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ALA A   9 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL A  10 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 15
        2.52 -     3.11: 5271
        3.11 -     3.71: 9978
        3.71 -     4.30: 14373
        4.30 -     4.90: 23998
  Nonbonded interactions: 53635
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  57 "
            pdb=" ND1 HIS B  58 "
     model   vdw
     1.925 3.120
  nonbonded pdb=" O   LEU B  57 "
            pdb=" CG  HIS B  58 "
     model   vdw
     2.275 3.260
  nonbonded pdb=" ND2 ASN A 122 "
            pdb=" O   GLY A 156 "
     model   vdw
     2.389 3.120
  nonbonded pdb=" N   ASN C  53 "
            pdb=" N   LEU C  54 "
     model   vdw
     2.414 2.560
  nonbonded pdb=" N   GLN B   8 "
            pdb=" OE1 GLN B   8 "
     model   vdw
     2.433 3.120
  ... (remaining 53630 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 'B'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and resid 2 through 243)
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.120
  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:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.800
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
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      :  0.012   0.077   7188  Z= 0.753
  Angle     :  1.620  13.181   9733  Z= 1.194
  Chirality :  0.103   0.445   1189
  Planarity :  0.007   0.061   1236
  Dihedral  : 12.729  85.909   2658
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.90 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  5.40 %
    Favored  : 93.41 %
  Cbeta Deviations :  0.93 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.27), residues: 923
  helix:  0.39 (0.22), residues: 555
  sheet: -2.83 (0.63), residues: 51
  loop : -1.82 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 113 
 HIS   0.008   0.002   HIS C  10 
 PHE   0.043   0.004   PHE C  35 
 TYR   0.033   0.003   TYR C  11 
 ARG   0.007   0.001   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.849 
Fit side-chains
REVERT: B  120 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: C  234 GLN cc_start: 0.7566 (mp10) cc_final: 0.7359 (mp10)
REVERT: D   62 LYS cc_start: 0.7391 (mtmt) cc_final: 0.7145 (mmmt)
  outliers start: 9
  outliers final: 5
  residues processed: 137
  average time/residue: 0.3017
  time to fit residues: 50.4861
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain D residue   40 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.0000
   chunk 69 optimal weight:    0.0670
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0470
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0870
   overall best weight:    0.1798

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
B  58 HIS
B  69 ASN
B 151 ASN
C  68 GLN
D 229 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7188  Z= 0.187
  Angle     :  0.618   6.824   9733  Z= 0.330
  Chirality :  0.041   0.150   1189
  Planarity :  0.004   0.033   1236
  Dihedral  :  5.540  53.047   1019
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.35 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.27), residues: 923
  helix:  0.97 (0.22), residues: 562
  sheet: -1.53 (0.57), residues: 75
  loop : -1.47 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 113 
 HIS   0.013   0.002   HIS B  58 
 PHE   0.023   0.002   PHE B   6 
 TYR   0.011   0.001   TYR B 192 
 ARG   0.004   0.001   ARG B 154 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8348 (ptmm) cc_final: 0.8038 (ttpt)
REVERT: B  120 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7550 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2592
  time to fit residues: 34.9177
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0370
   chunk 23 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 90 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7188  Z= 0.206
  Angle     :  0.558   6.788   9733  Z= 0.297
  Chirality :  0.040   0.151   1189
  Planarity :  0.004   0.033   1236
  Dihedral  :  5.112  55.264   1014
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.54 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.28), residues: 923
  helix:  1.13 (0.22), residues: 563
  sheet: -1.33 (0.64), residues: 71
  loop : -1.46 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 113 
 HIS   0.004   0.001   HIS B  58 
 PHE   0.011   0.001   PHE D  92 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.006   0.000   ARG C 121 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A   16 MET cc_start: 0.7950 (mmp) cc_final: 0.7698 (mmp)
REVERT: A   17 LYS cc_start: 0.8431 (ptmm) cc_final: 0.8109 (ttpt)
REVERT: A   58 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7293 (m90)
REVERT: A  210 LEU cc_start: 0.8167 (tp) cc_final: 0.7850 (mt)
REVERT: A  223 ARG cc_start: 0.6753 (ttm170) cc_final: 0.6465 (ttm170)
REVERT: B   58 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6461 (m90)
  outliers start: 16
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2635
  time to fit residues: 31.4031
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   58 HIS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7188  Z= 0.230
  Angle     :  0.558   7.651   9733  Z= 0.294
  Chirality :  0.040   0.138   1189
  Planarity :  0.004   0.038   1236
  Dihedral  :  4.985  56.179   1012
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.38 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.28), residues: 923
  helix:  1.25 (0.22), residues: 563
  sheet: -1.23 (0.65), residues: 71
  loop : -1.50 (0.34), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 113 
 HIS   0.020   0.002   HIS B  58 
 PHE   0.012   0.001   PHE D  92 
 TYR   0.011   0.001   TYR A 193 
 ARG   0.005   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8168 (ttpt)
REVERT: A   58 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7185 (m90)
REVERT: A   96 SER cc_start: 0.8626 (t) cc_final: 0.8330 (p)
REVERT: A  193 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.5905 (p90)
REVERT: A  210 LEU cc_start: 0.8158 (tp) cc_final: 0.7875 (mt)
REVERT: A  223 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6505 (ttm170)
REVERT: C   85 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6657 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 85
  average time/residue: 0.2804
  time to fit residues: 29.8008
Evaluate side-chains
  84 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0570
   chunk 66 optimal weight:    0.0370
   chunk 36 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.2774

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7188  Z= 0.139
  Angle     :  0.519  11.010   9733  Z= 0.273
  Chirality :  0.038   0.138   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  4.753  57.580   1012
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.44 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.29), residues: 923
  helix:  1.55 (0.23), residues: 563
  sheet: -1.19 (0.64), residues: 73
  loop : -1.39 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP D 113 
 HIS   0.005   0.001   HIS B  58 
 PHE   0.009   0.001   PHE A  65 
 TYR   0.008   0.001   TYR A 193 
 ARG   0.001   0.000   ARG C 207 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8406 (ptmm) cc_final: 0.8119 (ttpt)
REVERT: A   58 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7184 (m90)
REVERT: A   96 SER cc_start: 0.8631 (t) cc_final: 0.8405 (p)
REVERT: A  193 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.5922 (p90)
REVERT: A  194 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7150 (ttp-170)
REVERT: A  210 LEU cc_start: 0.8083 (tp) cc_final: 0.7832 (mt)
REVERT: A  223 ARG cc_start: 0.6624 (ttm170) cc_final: 0.6386 (ttm170)
REVERT: B   58 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6593 (m-70)
REVERT: C   85 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6531 (mp)
  outliers start: 14
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2822
  time to fit residues: 31.6343
Evaluate side-chains
  87 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   58 HIS
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0980
   chunk 21 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0980
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7188  Z= 0.150
  Angle     :  0.522  10.861   9733  Z= 0.273
  Chirality :  0.038   0.136   1189
  Planarity :  0.004   0.038   1236
  Dihedral  :  4.663  58.853   1012
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.89 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.29), residues: 923
  helix:  1.61 (0.23), residues: 565
  sheet: -1.12 (0.63), residues: 73
  loop : -1.40 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 113 
 HIS   0.002   0.000   HIS B  58 
 PHE   0.010   0.001   PHE A  65 
 TYR   0.008   0.001   TYR A 193 
 ARG   0.005   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   58 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7222 (m90)
REVERT: A   96 SER cc_start: 0.8706 (t) cc_final: 0.8500 (p)
REVERT: A  193 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.5917 (p90)
REVERT: A  210 LEU cc_start: 0.8104 (tp) cc_final: 0.7887 (mt)
REVERT: A  223 ARG cc_start: 0.6622 (ttm170) cc_final: 0.6367 (ttm170)
REVERT: C   85 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6572 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 87
  average time/residue: 0.2519
  time to fit residues: 28.0468
Evaluate side-chains
  86 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9980
   chunk 88 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0770
   chunk 35 optimal weight:    0.0030
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.2706

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
B  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7188  Z= 0.137
  Angle     :  0.516  10.932   9733  Z= 0.270
  Chirality :  0.038   0.135   1189
  Planarity :  0.004   0.039   1236
  Dihedral  :  4.599  59.603   1012
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.83 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 923
  helix:  1.70 (0.23), residues: 567
  sheet: -1.11 (0.62), residues: 73
  loop : -1.39 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 113 
 HIS   0.006   0.001   HIS D 232 
 PHE   0.009   0.001   PHE B  79 
 TYR   0.007   0.001   TYR A 193 
 ARG   0.005   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   58 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7252 (m90)
REVERT: A   96 SER cc_start: 0.8668 (t) cc_final: 0.8467 (p)
REVERT: A  193 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.5857 (p90)
REVERT: A  210 LEU cc_start: 0.8029 (tp) cc_final: 0.7818 (mt)
REVERT: A  223 ARG cc_start: 0.6596 (ttm170) cc_final: 0.6264 (ttm170)
REVERT: B  223 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7354 (mtp-110)
REVERT: C   85 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6500 (mp)
REVERT: D   40 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.4840 (t80)
REVERT: D  127 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8623 (tm-30)
  outliers start: 18
  outliers final: 6
  residues processed: 96
  average time/residue: 0.2662
  time to fit residues: 32.4412
Evaluate side-chains
  90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   58 HIS
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0570
   chunk 77 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7188  Z= 0.204
  Angle     :  0.549  10.854   9733  Z= 0.288
  Chirality :  0.040   0.159   1189
  Planarity :  0.004   0.038   1236
  Dihedral  :  4.707  59.938   1012
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.36 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.29), residues: 923
  helix:  1.66 (0.23), residues: 565
  sheet: -1.29 (0.61), residues: 74
  loop : -1.41 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 113 
 HIS   0.018   0.002   HIS B  58 
 PHE   0.011   0.001   PHE D  92 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A   58 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7239 (m90)
REVERT: A  193 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.5791 (p90)
REVERT: A  210 LEU cc_start: 0.8132 (tp) cc_final: 0.7918 (mt)
REVERT: A  223 ARG cc_start: 0.6721 (ttm170) cc_final: 0.6464 (ttm170)
REVERT: B    6 PHE cc_start: 0.8039 (t80) cc_final: 0.7715 (t80)
REVERT: B  223 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7413 (mtp-110)
REVERT: C   85 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6741 (mt)
REVERT: C  186 ASP cc_start: 0.8278 (t0) cc_final: 0.7994 (t0)
REVERT: D  182 GLU cc_start: 0.8309 (tp30) cc_final: 0.8108 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 88
  average time/residue: 0.2632
  time to fit residues: 29.3268
Evaluate side-chains
  89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0030
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0870
   chunk 54 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.3968

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

Flipped N/Q/H residues before XYZ refinement:
B  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7188  Z= 0.160
  Angle     :  0.537  10.619   9733  Z= 0.281
  Chirality :  0.039   0.154   1189
  Planarity :  0.004   0.038   1236
  Dihedral  :  4.644  59.126   1012
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.49 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.29), residues: 923
  helix:  1.75 (0.23), residues: 565
  sheet: -1.31 (0.61), residues: 74
  loop : -1.36 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 113 
 HIS   0.002   0.000   HIS B  58 
 PHE   0.010   0.001   PHE B  79 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   58 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7231 (m90)
REVERT: A  193 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.5780 (p90)
REVERT: A  194 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.7035 (ttp-170)
REVERT: A  210 LEU cc_start: 0.8057 (tp) cc_final: 0.7851 (mt)
REVERT: A  223 ARG cc_start: 0.6663 (ttm170) cc_final: 0.6404 (ttm170)
REVERT: B    6 PHE cc_start: 0.8050 (t80) cc_final: 0.7722 (t80)
REVERT: B  223 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7288 (mtp-110)
REVERT: C    7 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7677 (m)
REVERT: C   85 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6610 (mt)
  outliers start: 12
  outliers final: 6
  residues processed: 91
  average time/residue: 0.2882
  time to fit residues: 32.7050
Evaluate side-chains
  91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0870
   chunk 91 optimal weight:    4.9990
   chunk 84 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.5758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7188  Z= 0.174
  Angle     :  0.545  10.628   9733  Z= 0.285
  Chirality :  0.039   0.135   1189
  Planarity :  0.004   0.037   1236
  Dihedral  :  4.642  57.898   1012
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.02 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.29), residues: 923
  helix:  1.73 (0.23), residues: 565
  sheet: -1.35 (0.61), residues: 74
  loop : -1.38 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 113 
 HIS   0.001   0.000   HIS C 200 
 PHE   0.010   0.001   PHE A  65 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 223 

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8264 (tttm) cc_final: 0.7913 (ttmt)
REVERT: A   58 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7213 (m90)
REVERT: A  193 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.5745 (p90)
REVERT: A  210 LEU cc_start: 0.8088 (tp) cc_final: 0.7821 (mt)
REVERT: A  223 ARG cc_start: 0.6737 (ttm170) cc_final: 0.6475 (ttm170)
REVERT: C    7 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7653 (m)
REVERT: C   85 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6686 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 88
  average time/residue: 0.2620
  time to fit residues: 29.2204
Evaluate side-chains
  90 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  193 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   58 HIS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain D residue  215 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 64 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.109295 restraints weight = 9382.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.58
r_work: 0.3232 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7188  Z= 0.177
  Angle     :  0.554  10.578   9733  Z= 0.289
  Chirality :  0.039   0.135   1189
  Planarity :  0.004   0.038   1236
  Dihedral  :  4.649  57.432   1012
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.28 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.29), residues: 923
  helix:  1.76 (0.23), residues: 565
  sheet: -1.33 (0.61), residues: 74
  loop : -1.36 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 113 
 HIS   0.001   0.000   HIS C 200 
 PHE   0.010   0.001   PHE B  79 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B 223 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1775.64 seconds
wall clock time: 33 minutes 45.03 seconds (2025.03 seconds total)