Starting phenix.real_space_refine
on Tue Aug  6 14:27:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/08_2024/8wm8_37645.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    5396      2.51       5
     N    1374      2.21       5
     O    1459      1.98       5
     H    8522      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "D PHE   20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D TYR  115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  215": "OD1" <-> "OD2"
    Residue "D TYR  258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE   71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP   72": "OD1" <-> "OD2"
    Residue "B ASP  120": "OD1" <-> "OD2"
    Residue "B ASP  175": "OD1" <-> "OD2"
    Residue "B TYR  202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP  264": "OD1" <-> "OD2"
    Residue "A PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE    4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP    8": "OD1" <-> "OD2"
    Residue "C PHE   37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU   75": "OE1" <-> "OE2"
    Residue "C GLU  179": "OE1" <-> "OE2"
    Residue "C TYR  243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C TYR  252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 16776
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 4116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 4116
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 4198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4198
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 17, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 4170
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 17, 'TRANS': 245}
    Chain: "C"
      Number of atoms: 4288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4288
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 11, 'TRANS': 256}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'NO3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.93, per 1000 atoms: 0.47
  Number of scatterers: 16776
  At special positions: 0
  Unit cell: (81.32, 118.77, 95.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     O    1459      8.00
     N    1374      7.00
     C    5396      6.00
     H    8522      1.00
    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: 13.76
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      56.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'D' and resid 62 through 71
    Processing helix  chain 'D' and resid 83 through 86
    Processing helix  chain 'D' and resid 100 through 104
      removed outlier: 3.852A  pdb=" N   CYS D 103 " --> pdb=" O   GLN D 100 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LEU D 104 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 104'
    Processing helix  chain 'D' and resid 109 through 119
      removed outlier: 4.008A  pdb=" N   ALA D 117 " --> pdb=" O   ASN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 140
      removed outlier: 3.710A  pdb=" N   ALA D 132 " --> pdb=" O   ALA D 128 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG D 135 " --> pdb=" O   ARG D 131 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET D 140 " --> pdb=" O   GLU D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 170
      removed outlier: 3.663A  pdb=" N   GLN D 160 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ARG D 161 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL D 162 " --> pdb=" O   MET D 158 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE D 170 " --> pdb=" O   ARG D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 204
      removed outlier: 3.548A  pdb=" N   GLU D 191 " --> pdb=" O   ILE D 187 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN D 193 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLU D 194 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU D 195 " --> pdb=" O   GLU D 191 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN D 198 " --> pdb=" O   GLU D 194 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ILE D 199 " --> pdb=" O   GLU D 195 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS D 203 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 221
    Processing helix  chain 'D' and resid 256 through 271
      removed outlier: 3.769A  pdb=" N   ASP D 260 " --> pdb=" O   PRO D 256 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 23
      removed outlier: 3.643A  pdb=" N   ASN B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TRP B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 44
      removed outlier: 3.553A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.686A  pdb=" N   PHE B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B  66 " --> pdb=" O   TRP B  62 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B  67 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 67'
    Processing helix  chain 'B' and resid 80 through 94
      removed outlier: 3.832A  pdb=" N   SER B  87 " --> pdb=" O   GLN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 111
      removed outlier: 3.823A  pdb=" N   ILE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 129
      removed outlier: 4.034A  pdb=" N   ALA B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
      removed outlier: 4.340A  pdb=" N   VAL B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU B 126 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 134 through 142
    Processing helix  chain 'B' and resid 145 through 155
      removed outlier: 3.664A  pdb=" N   ILE B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   PHE B 151 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.871A  pdb=" N   ASN B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY B 168 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 183
      removed outlier: 3.620A  pdb=" N   ILE B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 195
    Processing helix  chain 'B' and resid 195 through 208
      Proline residue:  B 201  - end of helix
    Processing helix  chain 'B' and resid 208 through 219
      removed outlier: 3.804A  pdb=" N   GLY B 212 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B 213 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.610A  pdb=" N   ASN B 239 " --> pdb=" O   TRP B 235 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   THR B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 235 through 240'
    Processing helix  chain 'B' and resid 244 through 275
      removed outlier: 3.950A  pdb=" N   GLU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 249 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B 253 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY B 268 " --> pdb=" O   ASP B 264 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 274 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 26 through 44
    Processing helix  chain 'A' and resid 53 through 60
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 89 through 94
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 3.530A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 104 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 144 through 157
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 4.024A  pdb=" N   ASN A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.549A  pdb=" N   ILE A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 199 through 214
      removed outlier: 3.569A  pdb=" N   THR A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   GLY A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.736A  pdb=" N   VAL A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.562A  pdb=" N   LEU A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.697A  pdb=" N   VAL A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 57
      removed outlier: 3.534A  pdb=" N   ILE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 94 through 105
      removed outlier: 3.507A  pdb=" N   VAL C  99 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA C 100 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA C 102 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 123
      removed outlier: 3.745A  pdb=" N   ALA C 117 " --> pdb=" O   GLY C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 155
      removed outlier: 3.805A  pdb=" N   ARG C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL C 147 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA C 148 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 186
      removed outlier: 3.825A  pdb=" N   GLU C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLN C 180 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 203
      removed outlier: 3.837A  pdb=" N   ALA C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 238
      removed outlier: 3.831A  pdb=" N   VAL C 238 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 269
      removed outlier: 4.187A  pdb=" N   TYR C 244 " --> pdb=" O   HIS C 240 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN C 245 " --> pdb=" O   PRO C 241 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU C 249 " --> pdb=" O   ASN C 245 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA C 268 " --> pdb=" O   GLN C 264 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 47
      removed outlier: 6.433A  pdb=" N   LYS D  28 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ASP D  41 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL D  26 " --> pdb=" O   ASP D  41 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE D  43 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU D  24 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU D  45 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL D  22 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU D  24 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL D  80 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 98
      removed outlier: 3.518A  pdb=" N   LEU D 208 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   VAL D 225 " --> pdb=" O   PHE D  52 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   CYS D  54 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 25
      removed outlier: 6.529A  pdb=" N   ARG C  12 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   HIS C   9 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY C  65 " --> pdb=" O   HIS C   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162
      removed outlier: 7.129A  pdb=" N   LEU C 162 " --> pdb=" O   VAL C 195 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   SER C  39 " --> pdb=" O   VAL C 210 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    927 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: 5.39

  Time building geometry restraints manager: 14.36 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8514
        1.03 -     1.23: 9
        1.23 -     1.42: 3400
        1.42 -     1.62: 4997
        1.62 -     1.81: 42
  Bond restraints: 16962
  Sorted by residual:
  bond pdb=" N   NO3 A 301 "
       pdb=" O3  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.84e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O2  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O1  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.263 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C   ILE B 209 "
       pdb=" O   ILE B 209 "
    ideal  model  delta    sigma   weight residual
    1.241  1.228  0.013 1.19e-02 7.06e+03 1.28e+00
  bond pdb=" C   GLY D  35 "
       pdb=" N   PRO D  36 "
    ideal  model  delta    sigma   weight residual
    1.333  1.343 -0.010 1.01e-02 9.80e+03 9.72e-01
  ... (remaining 16957 not shown)

  Histogram of bond angle deviations from ideal:
      100.43 -   107.15: 428
      107.15 -   113.86: 20739
      113.86 -   120.58: 5468
      120.58 -   127.29: 4135
      127.29 -   134.01: 108
  Bond angle restraints: 30878
  Sorted by residual:
  angle pdb=" N   SER A  96 "
        pdb=" CA  SER A  96 "
        pdb=" C   SER A  96 "
      ideal   model   delta    sigma   weight residual
     113.41  107.47    5.94 1.22e+00 6.72e-01 2.37e+01
  angle pdb=" N   ASN A 117 "
        pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
      ideal   model   delta    sigma   weight residual
     114.62  109.17    5.45 1.14e+00 7.69e-01 2.28e+01
  angle pdb=" N   VAL C 106 "
        pdb=" CA  VAL C 106 "
        pdb=" C   VAL C 106 "
      ideal   model   delta    sigma   weight residual
     111.62  108.23    3.39 7.90e-01 1.60e+00 1.84e+01
  angle pdb=" N   ASP D 178 "
        pdb=" CA  ASP D 178 "
        pdb=" C   ASP D 178 "
      ideal   model   delta    sigma   weight residual
     110.41  106.28    4.13 1.23e+00 6.61e-01 1.13e+01
  angle pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
        pdb=" N   ALA A 118 "
      ideal   model   delta    sigma   weight residual
     119.71  116.30    3.41 1.17e+00 7.31e-01 8.47e+00
  ... (remaining 30873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7061
       17.96 -    35.92: 570
       35.92 -    53.88: 221
       53.88 -    71.84: 37
       71.84 -    89.80: 16
  Dihedral angle restraints: 7905
    sinusoidal: 4361
      harmonic: 3544
  Sorted by residual:
  dihedral pdb=" CA  TRP A 235 "
           pdb=" C   TRP A 235 "
           pdb=" N   ASP A 236 "
           pdb=" CA  ASP A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  SER A 157 "
           pdb=" C   SER A 157 "
           pdb=" N   ILE A 158 "
           pdb=" CA  ILE A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A  23 "
           pdb=" C   TRP A  23 "
           pdb=" N   LYS A  24 "
           pdb=" CA  LYS A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.16   19.84     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 7902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 851
       0.030 -    0.059: 303
       0.059 -    0.089: 118
       0.089 -    0.118: 62
       0.118 -    0.148: 13
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ILE B 172 "
            pdb=" N   ILE B 172 "
            pdb=" C   ILE B 172 "
            pdb=" CB  ILE B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  ILE A 172 "
            pdb=" N   ILE A 172 "
            pdb=" C   ILE A 172 "
            pdb=" CB  ILE A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE D 241 "
            pdb=" N   ILE D 241 "
            pdb=" C   ILE D 241 "
            pdb=" CB  ILE D 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1344 not shown)

  Planarity restraints: 2447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 112 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO A 113 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 146 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO B 147 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 245 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO D 246 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 246 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 246 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2444 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 795
        2.18 -     2.78: 34458
        2.78 -     3.39: 46449
        3.39 -     3.99: 59381
        3.99 -     4.60: 92618
  Nonbonded interactions: 233701
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 160 "
            pdb="HD21 ASN A 164 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" OD1 ASP D 267 "
            pdb="HD21 ASN D 271 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" O   PHE D 219 "
            pdb="HH11 ARG D 247 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASN D 263 "
            pdb=" HH  TYR C 244 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" OD1 ASP C   8 "
            pdb=" HD1 HIS C   9 "
     model   vdw
     1.675 2.450
  ... (remaining 233696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 15 through 277)
  selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ 
 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  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:             0.250
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     55.270
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
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      :  0.002   0.044   8440  Z= 0.155
  Angle     :  0.581   5.941  11494  Z= 0.328
  Chirality :  0.040   0.148   1347
  Planarity :  0.004   0.046   1458
  Dihedral  : 14.853  89.805   3077
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.26), residues: 1047
  helix: -1.14 (0.24), residues: 517
  sheet: -2.40 (0.66), residues: 66
  loop : -2.07 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C 240 
 PHE   0.015   0.001   PHE D  20 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.004   0.000   ARG A 127 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.3628
  time to fit residues: 97.0400
Evaluate side-chains
  150 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
B 164 ASN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8440  Z= 0.252
  Angle     :  0.645   6.587  11494  Z= 0.337
  Chirality :  0.043   0.143   1347
  Planarity :  0.005   0.053   1458
  Dihedral  :  5.195  25.161   1122
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.55 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.03 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.25), residues: 1047
  helix: -1.10 (0.22), residues: 527
  sheet: -2.70 (0.62), residues: 65
  loop : -2.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 159 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.018   0.002   TYR A 116 
 ARG   0.005   0.000   ARG C 129 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  176 TYR cc_start: 0.8330 (m-10) cc_final: 0.7597 (m-10)
REVERT: A  236 ASP cc_start: 0.7773 (t0) cc_final: 0.7515 (t0)
REVERT: C   75 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7407 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 164
  average time/residue: 0.3504
  time to fit residues: 84.4015
Evaluate side-chains
  156 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.204
  Angle     :  0.594   6.331  11494  Z= 0.310
  Chirality :  0.042   0.149   1347
  Planarity :  0.005   0.056   1458
  Dihedral  :  5.147  25.312   1122
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.07 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.81 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.25), residues: 1047
  helix: -1.06 (0.22), residues: 542
  sheet: -2.65 (0.63), residues: 60
  loop : -2.33 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.004   0.001   HIS C 197 
 PHE   0.014   0.001   PHE A  95 
 TYR   0.011   0.001   TYR B 238 
 ARG   0.004   0.000   ARG C 129 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7801 (t0) cc_final: 0.7576 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 161
  average time/residue: 0.3387
  time to fit residues: 81.2039
Evaluate side-chains
  154 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 149
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  171 GLN
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.192
  Angle     :  0.578   6.272  11494  Z= 0.299
  Chirality :  0.042   0.146   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.102  25.381   1122
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.97 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 13.04 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.25), residues: 1047
  helix: -0.95 (0.22), residues: 541
  sheet: -2.60 (0.60), residues: 70
  loop : -2.31 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.003   0.001   HIS C  43 
 PHE   0.021   0.001   PHE A 154 
 TYR   0.024   0.001   TYR A 116 
 ARG   0.004   0.000   ARG C 129 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 THR cc_start: 0.8732 (t) cc_final: 0.8528 (t)
REVERT: A  236 ASP cc_start: 0.7803 (t0) cc_final: 0.7582 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 158
  average time/residue: 0.3415
  time to fit residues: 80.0200
Evaluate side-chains
  153 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8440  Z= 0.262
  Angle     :  0.601   6.753  11494  Z= 0.312
  Chirality :  0.042   0.149   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.204  25.459   1122
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.83 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.72 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.25), residues: 1047
  helix: -0.97 (0.22), residues: 542
  sheet: -2.72 (0.58), residues: 70
  loop : -2.35 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C 122 
 PHE   0.020   0.001   PHE A  95 
 TYR   0.014   0.001   TYR B 176 
 ARG   0.003   0.000   ARG C 129 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 7
  residues processed: 150
  average time/residue: 0.3468
  time to fit residues: 78.5396
Evaluate side-chains
  150 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8440  Z= 0.251
  Angle     :  0.601   6.638  11494  Z= 0.312
  Chirality :  0.042   0.149   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.231  25.837   1122
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.16 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.25), residues: 1047
  helix: -0.99 (0.22), residues: 548
  sheet: -2.78 (0.58), residues: 71
  loop : -2.31 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C  43 
 PHE   0.018   0.001   PHE A  95 
 TYR   0.012   0.001   TYR B 176 
 ARG   0.004   0.000   ARG C 234 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7780 (t0) cc_final: 0.7488 (t0)
  outliers start: 9
  outliers final: 9
  residues processed: 148
  average time/residue: 0.3536
  time to fit residues: 77.4409
Evaluate side-chains
  149 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 72 optimal weight:    0.4980
   chunk 83 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8440  Z= 0.186
  Angle     :  0.574   6.181  11494  Z= 0.296
  Chirality :  0.041   0.152   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.130  25.396   1122
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.39 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.26), residues: 1047
  helix: -0.82 (0.23), residues: 541
  sheet: -2.73 (0.59), residues: 71
  loop : -2.21 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.003   0.001   HIS C 122 
 PHE   0.016   0.001   PHE A 154 
 TYR   0.010   0.001   TYR B 238 
 ARG   0.005   0.000   ARG C 234 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7797 (t0) cc_final: 0.7584 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 156
  average time/residue: 0.3440
  time to fit residues: 80.5502
Evaluate side-chains
  153 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8440  Z= 0.215
  Angle     :  0.581   6.687  11494  Z= 0.300
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  5.140  25.591   1122
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.12 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.72 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.26), residues: 1047
  helix: -0.75 (0.23), residues: 541
  sheet: -2.76 (0.59), residues: 71
  loop : -2.20 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.003   0.001   HIS C 197 
 PHE   0.015   0.001   PHE A 154 
 TYR   0.010   0.001   TYR B 238 
 ARG   0.004   0.000   ARG C 234 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7814 (t0) cc_final: 0.7595 (t0)
  outliers start: 10
  outliers final: 10
  residues processed: 149
  average time/residue: 0.3336
  time to fit residues: 74.5728
Evaluate side-chains
  151 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0980
   chunk 95 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.191
  Angle     :  0.578   6.985  11494  Z= 0.298
  Chirality :  0.042   0.150   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  5.102  25.442   1122
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.26 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.50 %
    Favored  : 82.27 %
  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: -2.15 (0.26), residues: 1047
  helix: -0.64 (0.23), residues: 541
  sheet: -2.70 (0.59), residues: 71
  loop : -2.15 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS D 275 
 PHE   0.016   0.001   PHE A 154 
 TYR   0.018   0.001   TYR D 102 
 ARG   0.005   0.000   ARG C 234 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7800 (t0) cc_final: 0.7577 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 150
  average time/residue: 0.3249
  time to fit residues: 72.7786
Evaluate side-chains
  154 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8440  Z= 0.199
  Angle     :  0.581   7.229  11494  Z= 0.299
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  5.079  25.438   1122
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.50 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.26), residues: 1047
  helix: -0.60 (0.23), residues: 541
  sheet: -2.73 (0.59), residues: 71
  loop : -2.17 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS D 275 
 PHE   0.016   0.001   PHE A 154 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.005   0.000   ARG C 234 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7788 (t0) cc_final: 0.7560 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 155
  average time/residue: 0.3509
  time to fit residues: 80.2793
Evaluate side-chains
  160 residues out of total 897 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 12 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0670
   chunk 81 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   chunk 71 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.150206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117318 restraints weight = 34567.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123175 restraints weight = 15699.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126810 restraints weight = 9714.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8440  Z= 0.165
  Angle     :  0.575   7.185  11494  Z= 0.294
  Chirality :  0.042   0.150   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  4.990  25.001   1122
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.95 %
    Favored  : 81.72 %
  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: -1.95 (0.26), residues: 1047
  helix: -0.46 (0.23), residues: 553
  sheet: -2.64 (0.59), residues: 71
  loop : -2.10 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.008   0.001   HIS D 137 
 PHE   0.017   0.001   PHE A 154 
 TYR   0.012   0.001   TYR D 102 
 ARG   0.005   0.000   ARG C 234 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3610.43 seconds
wall clock time: 63 minutes 30.98 seconds (3810.98 seconds total)