Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 15:31:42 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_23752.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_23752.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_23752.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_23752.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/04_2022/7mc0_23752.pdb"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   19": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  152": "OE1" <-> "OE2"
    Residue "B GLU  125": "OE1" <-> "OE2"
    Residue "B ARG  223": "NH1" <-> "NH2"
    Residue "C GLU   23": "OE1" <-> "OE2"
    Residue "C GLU  109": "OE1" <-> "OE2"
    Residue "C GLU  182": "OE1" <-> "OE2"
    Residue "D ASP   31": "OD1" <-> "OD2"
    Residue "D GLU   33": "OE1" <-> "OE2"
    Residue "D ARG  121": "NH1" <-> "NH2"
    Residue "D GLU  124": "OE1" <-> "OE2"
    Residue "D GLU  167": "OE1" <-> "OE2"
    Residue "D GLU  182": "OE1" <-> "OE2"
    Residue "D GLU  185": "OE1" <-> "OE2"
    Residue "D GLU  201": "OE1" <-> "OE2"
    Residue "D ARG  211": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 4.39, per 1000 atoms: 0.62
  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  - 3.50
        Amino acid           : False - 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: 2.65
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.36
  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: 1.91

  Time building geometry restraints manager: 2.90 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:
       99.08 -   106.11: 169
      106.11 -   113.14: 3752
      113.14 -   120.16: 3289
      120.16 -   127.19: 2483
      127.19 -   134.22: 40
  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 2.520
  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 2.520
  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 2.520
  ... (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
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
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.
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:             1.680
  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:          10.210
  Check model and map are aligned:         0.110
  Convert atoms to be neutral:             0.060
  Process input model:                     22.800
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
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 %
  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

*********************** 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 fitting.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.794 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 137
  average time/residue: 0.2663
  time to fit residues: 44.9794
Evaluate side-chains
  85 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.842 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1595
  time to fit residues: 2.2421
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.0030
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.6190

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7188  Z= 0.222
  Angle     :  0.636   6.829   9733  Z= 0.341
  Chirality :  0.042   0.149   1189
  Planarity :  0.004   0.032   1236
  Dihedral  :  4.904  30.584   1008
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer Outliers :  1.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.27), residues: 923
  helix:  0.93 (0.22), residues: 562
  sheet: -1.50 (0.58), residues: 75
  loop : -1.62 (0.33), residues: 286

*********************** 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
  100 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.781 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 0.2446
  time to fit residues: 29.8829
Evaluate side-chains
  85 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0658
  time to fit residues: 1.8596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   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: 0.8134
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7188  Z= 0.233
  Angle     :  0.574   6.903   9733  Z= 0.304
  Chirality :  0.041   0.149   1189
  Planarity :  0.004   0.034   1236
  Dihedral  :  4.586  24.119   1008
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer Outliers :  1.19 %
  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:  0.02 (0.28), residues: 923
  helix:  1.04 (0.22), residues: 562
  sheet: -1.30 (0.65), residues: 71
  loop : -1.64 (0.33), residues: 290

*********************** 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
  88 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.849 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 86
  average time/residue: 0.2528
  time to fit residues: 27.7462
Evaluate side-chains
  75 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.810 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0766
  time to fit residues: 1.6426
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7188  Z= 0.214
  Angle     :  0.553   7.298   9733  Z= 0.291
  Chirality :  0.040   0.139   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  4.428  21.413   1008
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer Outliers :  1.45 %
  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:  0.17 (0.28), residues: 923
  helix:  1.18 (0.23), residues: 562
  sheet: -1.24 (0.66), residues: 71
  loop : -1.64 (0.34), residues: 290

*********************** 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
  84 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.827 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 80
  average time/residue: 0.2616
  time to fit residues: 26.6629
Evaluate side-chains
  74 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.764 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0647
  time to fit residues: 1.6602
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0030
   chunk 61 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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: 0.8120
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7188  Z= 0.181
  Angle     :  0.541  10.291   9733  Z= 0.283
  Chirality :  0.039   0.137   1189
  Planarity :  0.004   0.043   1236
  Dihedral  :  4.222  19.359   1008
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer Outliers :  0.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 923
  helix:  1.40 (0.23), residues: 562
  sheet: -1.11 (0.64), residues: 71
  loop : -1.66 (0.34), residues: 290

*********************** 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
  83 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.865 
Fit side-chains
  outliers start: 7
  outliers final: 2
  residues processed: 81
  average time/residue: 0.2765
  time to fit residues: 28.6889
Evaluate side-chains
  75 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0625
  time to fit residues: 1.2553
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 85 optimal weight:    0.3980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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: 0.8117
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7188  Z= 0.173
  Angle     :  0.531  10.113   9733  Z= 0.277
  Chirality :  0.039   0.137   1189
  Planarity :  0.004   0.042   1236
  Dihedral  :  4.130  19.048   1008
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer Outliers :  0.53 %
  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:  0.47 (0.29), residues: 923
  helix:  1.46 (0.23), residues: 564
  sheet: -1.02 (0.64), residues: 71
  loop : -1.67 (0.34), residues: 288

*********************** 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
  81 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.837 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 78
  average time/residue: 0.2645
  time to fit residues: 26.1549
Evaluate side-chains
  78 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.818 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0668
  time to fit residues: 1.4943
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   chunk 54 optimal weight:    0.0000
   chunk 40 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.3122

-------------------------------------------------------------------------------
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: 0.8073
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7188  Z= 0.142
  Angle     :  0.527  10.403   9733  Z= 0.273
  Chirality :  0.038   0.135   1189
  Planarity :  0.004   0.041   1236
  Dihedral  :  3.962  17.301   1008
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer Outliers :  0.40 %
  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:  0.67 (0.29), residues: 923
  helix:  1.65 (0.23), residues: 564
  sheet: -1.01 (0.63), residues: 71
  loop : -1.62 (0.34), residues: 288

*********************** 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
  87 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.842 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 86
  average time/residue: 0.2699
  time to fit residues: 29.2664
Evaluate side-chains
  78 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.822 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0612
  time to fit residues: 1.2205
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0980
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   chunk 69 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 84 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3722

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= 0.162
  Angle     :  0.533  10.146   9733  Z= 0.277
  Chirality :  0.038   0.136   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  3.944  18.778   1008
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer Outliers :  0.26 %
  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:  0.69 (0.29), residues: 923
  helix:  1.65 (0.23), residues: 565
  sheet: -1.06 (0.62), residues: 71
  loop : -1.56 (0.35), residues: 287

*********************** 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
  83 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.873 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 81
  average time/residue: 0.2753
  time to fit residues: 28.4284
Evaluate side-chains
  81 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.840 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0745
  time to fit residues: 1.4370
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 84 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0010
   chunk 54 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0970
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.3384

-------------------------------------------------------------------------------
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: 0.8074
moved from start:          0.3834

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= 0.147
  Angle     :  0.529  10.016   9733  Z= 0.276
  Chirality :  0.038   0.135   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  3.881  18.669   1008
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer Outliers :  0.13 %
  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: -0.99 (0.62), residues: 71
  loop : -1.51 (0.35), residues: 287

*********************** 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
  79 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.911 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2662
  time to fit residues: 26.4901
Evaluate side-chains
  79 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1706
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0980
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3868

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= 0.172
  Angle     :  0.546  10.101   9733  Z= 0.285
  Chirality :  0.039   0.136   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  3.902  19.403   1008
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer Outliers :  0.26 %
  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:  1.75 (0.23), residues: 565
  sheet: -1.05 (0.61), residues: 71
  loop : -1.51 (0.35), residues: 287

********************** 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
  81 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.835 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2654
  time to fit residues: 26.7965
Evaluate side-chains
  79 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.880 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0718
  time to fit residues: 1.4646
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0770
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.133313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.110481 restraints weight = 9372.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.57
r_work: 0.3364 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 2.33 restraints_weight: 0.2500
r_work: 0.3342 rms_B_bonded: 2.36 restraints_weight: 0.1250
r_work: 0.3330 rms_B_bonded: 2.43 restraints_weight: 0.0625
r_work: 0.3317 rms_B_bonded: 2.54 restraints_weight: 0.0312
r_work: 0.3303 rms_B_bonded: 2.67 restraints_weight: 0.0156
r_work: 0.3289 rms_B_bonded: 2.84 restraints_weight: 0.0078
r_work: 0.3274 rms_B_bonded: 3.04 restraints_weight: 0.0039
r_work: 0.3258 rms_B_bonded: 3.27 restraints_weight: 0.0020
r_work: 0.3241 rms_B_bonded: 3.54 restraints_weight: 0.0010
r_work: 0.3223 rms_B_bonded: 3.84 restraints_weight: 0.0005
r_work: 0.3204 rms_B_bonded: 4.19 restraints_weight: 0.0002
r_work: 0.3183 rms_B_bonded: 4.57 restraints_weight: 0.0001
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3948

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= 0.153
  Angle     :  0.535   9.935   9733  Z= 0.279
  Chirality :  0.038   0.135   1189
  Planarity :  0.004   0.040   1236
  Dihedral  :  3.832  18.999   1008
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer Outliers :  0.13 %
  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:  0.90 (0.29), residues: 923
  helix:  1.82 (0.23), residues: 565
  sheet: -0.99 (0.62), residues: 71
  loop : -1.49 (0.36), residues: 287

===============================================================================
Job complete
usr+sys time: 1575.31 seconds
wall clock time: 29 minutes 15.60 seconds (1755.60 seconds total)