Starting phenix.real_space_refine
on Thu Dec  7 18:27:07 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/12_2023/7u14_26277.pdb"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  246": "OE1" <-> "OE2"
    Residue "B GLU  246": "OE1" <-> "OE2"
    Residue "C GLU  246": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.90, per 1000 atoms: 1.13
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (98.808, 118.14, 33.294, 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      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 60.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 6.384A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 9.124A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.683A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   TYR A 135 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   TYR C 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.050A  pdb=" N   ALA B 131 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   SER C 134 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 9.677A  pdb=" N   ASP C 136 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   TYR B 135 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165
      removed outlier: 6.948A  pdb=" N   ILE A 146 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   THR B 147 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   THR B 149 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LEU A 150 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ASN B 151 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ILE A 152 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   THR B 153 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ASN A 154 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ASN B 155 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ASN A 156 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR A 158 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   SER B 159 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL A 160 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU B 161 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ILE B 146 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR C 147 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   THR C 149 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B 150 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ASN C 151 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE B 152 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   THR C 153 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ASN B 154 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ASN C 155 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ASN B 156 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   TYR B 158 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   SER C 159 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 160 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLU C 161 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.575A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.408A  pdb=" N   THR A 185 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR B 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 6.775A  pdb=" N   ILE A 195 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASP B 196 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TYR A 197 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   THR B 198 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE B 195 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ASP C 196 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   TYR B 197 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   THR C 198 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203
      removed outlier: 6.336A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219
      removed outlier: 6.973A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   PHE C 213 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 228
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.605A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR B 234 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   PHE C 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   TYR B 236 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   HIS C 239 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLY B 238 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   GLU C 241 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLN C 245 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER B 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253

    66 hydrogen bonds defined for protein.
    198 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: 0.81

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1011
        1.34 -     1.46: 629
        1.46 -     1.58: 1840
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C1  NAG C 304 "
       pdb=" O5  NAG C 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C1  NAG B 304 "
       pdb=" O5  NAG B 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CD  GLU A 206 "
       pdb=" OE1 GLU A 206 "
    ideal  model  delta    sigma   weight residual
    1.249  1.214  0.035 1.90e-02 2.77e+03 3.39e+00
  bond pdb=" CB  VAL C 225 "
       pdb=" CG2 VAL C 225 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.33e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
       99.66 -   105.99: 60
      105.99 -   112.32: 1842
      112.32 -   118.65: 975
      118.65 -   124.98: 1899
      124.98 -   131.31: 12
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CA  MET C 228 "
        pdb=" CB  MET C 228 "
        pdb=" CG  MET C 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" CA  MET A 228 "
        pdb=" CB  MET A 228 "
        pdb=" CG  MET A 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.51   -7.41 2.00e+00 2.50e-01 1.37e+01
  angle pdb=" CA  MET B 228 "
        pdb=" CB  MET B 228 "
        pdb=" CG  MET B 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.42   -7.32 2.00e+00 2.50e-01 1.34e+01
  angle pdb=" CA  GLU C 205 "
        pdb=" CB  GLU C 205 "
        pdb=" CG  GLU C 205 "
      ideal   model   delta    sigma   weight residual
     114.10  121.18   -7.08 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" CA  GLU B 205 "
        pdb=" CB  GLU B 205 "
        pdb=" CG  GLU B 205 "
      ideal   model   delta    sigma   weight residual
     114.10  121.12   -7.02 2.00e+00 2.50e-01 1.23e+01
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.61: 2043
       24.61 -    49.21: 178
       49.21 -    73.82: 29
       73.82 -    98.43: 18
       98.43 -   123.04: 3
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.17   52.83     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.18   52.82     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.24   52.76     1      1.00e+01 1.00e-02 3.79e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 477
       0.078 -    0.156: 117
       0.156 -    0.234: 9
       0.234 -    0.312: 0
       0.312 -    0.390: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CB  ILE C 203 "
            pdb=" CA  ILE C 203 "
            pdb=" CG1 ILE C 203 "
            pdb=" CG2 ILE C 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CB  ILE A 203 "
            pdb=" CA  ILE A 203 "
            pdb=" CG1 ILE A 203 "
            pdb=" CG2 ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.69e+00
  chirality pdb=" CB  ILE B 203 "
            pdb=" CA  ILE B 203 "
            pdb=" CG1 ILE B 203 "
            pdb=" CG2 ILE B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.66e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 125 "   -0.027 2.00e-02 2.50e+03   2.67e-02 1.43e+01
        pdb=" CG  TYR C 125 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 125 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 125 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 125 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 125 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 125 "   -0.027 2.00e-02 2.50e+03   2.66e-02 1.42e+01
        pdb=" CG  TYR A 125 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 125 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 125 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 125 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 125 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 125 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 125 "   -0.026 2.00e-02 2.50e+03   2.65e-02 1.41e+01
        pdb=" CG  TYR B 125 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 125 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 125 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 125 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 125 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 125 "    0.000 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1220
        2.87 -     3.38: 2979
        3.38 -     3.89: 6107
        3.89 -     4.39: 6044
        4.39 -     4.90: 11905
  Nonbonded interactions: 28255
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.369 2.520
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.369 2.520
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.370 2.520
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" O   HIS B 239 "
     model   vdw
     2.423 2.440
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   HIS A 239 "
     model   vdw
     2.424 2.440
  ... (remaining 28250 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' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'B' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'C' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  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:          4.020
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.210
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5068
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      :  0.006   0.074   3516  Z= 0.426
  Angle     :  0.945   8.455   4788  Z= 0.493
  Chirality :  0.066   0.390    606
  Planarity :  0.005   0.028    579
  Dihedral  : 19.585 123.035   1476
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  :  2.36 %
    Favored  : 91.34 %
  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: -3.07 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS C 222 
   PHE   0.020   0.004   PHE B 171 
   TYR   0.064   0.004   TYR C 125 
   ARG   0.002   0.000   ARG A 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 1
  residues processed: 72
  average time/residue: 0.1189
  time to fit residues: 11.0428
Evaluate side-chains
  42 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.362 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0619
  time to fit residues: 0.6200
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 GLN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 245 GLN
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 222 HIS
C 229 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN
C 245 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   3516  Z= 0.377
  Angle     :  0.932  10.725   4788  Z= 0.493
  Chirality :  0.065   0.376    606
  Planarity :  0.005   0.036    579
  Dihedral  : 14.090 107.818    711
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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: -3.51 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.002   HIS B 239 
   PHE   0.024   0.003   PHE A 171 
   TYR   0.021   0.004   TYR A 143 
   ARG   0.002   0.000   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.344 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1151
  time to fit residues: 8.2859
Evaluate side-chains
  40 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.352 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4844
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
moved from start:          0.6511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3516  Z= 0.297
  Angle     :  0.842   7.951   4788  Z= 0.441
  Chirality :  0.064   0.397    606
  Planarity :  0.004   0.032    579
  Dihedral  : 14.531 110.164    711
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.20 %
    Favored  : 95.54 %
  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: -3.54 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS B 239 
   PHE   0.021   0.003   PHE A 171 
   TYR   0.019   0.003   TYR B 143 
   ARG   0.002   0.000   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.419 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1329
  time to fit residues: 8.7952
Evaluate side-chains
  37 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.327 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4571
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:   30.0000
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 0 optimal weight:   10.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5965
moved from start:          0.7240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3516  Z= 0.314
  Angle     :  0.845   8.209   4788  Z= 0.437
  Chirality :  0.063   0.400    606
  Planarity :  0.004   0.028    579
  Dihedral  : 14.701 110.717    711
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -3.56 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.002   HIS A 239 
   PHE   0.021   0.003   PHE A 171 
   TYR   0.019   0.003   TYR B 157 
   ARG   0.002   0.000   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.571 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0881
  time to fit residues: 6.1937
Evaluate side-chains
  33 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.329 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4538
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    3.8126

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5994
moved from start:          0.7600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3516  Z= 0.289
  Angle     :  0.816   8.328   4788  Z= 0.418
  Chirality :  0.064   0.450    606
  Planarity :  0.004   0.025    579
  Dihedral  : 14.809 110.192    711
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 18.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  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: -3.76 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS C 239 
   PHE   0.019   0.003   PHE A 171 
   TYR   0.018   0.003   TYR C 125 
   ARG   0.004   0.000   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.338 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0948
  time to fit residues: 5.7975
Evaluate side-chains
  34 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.371 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4874
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6091
moved from start:          0.8141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3516  Z= 0.361
  Angle     :  0.903   8.938   4788  Z= 0.469
  Chirality :  0.068   0.508    606
  Planarity :  0.005   0.025    579
  Dihedral  : 14.772 109.877    711
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.78 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -3.97 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 239 
   PHE   0.032   0.004   PHE A 237 
   TYR   0.023   0.004   TYR B 157 
   ARG   0.003   0.001   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.374 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0928
  time to fit residues: 6.1072
Evaluate side-chains
  35 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.372 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6127
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 ASN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
moved from start:          0.8325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3516  Z= 0.288
  Angle     :  0.854   9.189   4788  Z= 0.438
  Chirality :  0.063   0.414    606
  Planarity :  0.004   0.023    579
  Dihedral  : 14.806 109.773    711
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  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: -3.97 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS C 239 
   PHE   0.021   0.003   PHE A 237 
   TYR   0.021   0.003   TYR C 125 
   ARG   0.003   0.000   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.388 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0909
  time to fit residues: 6.1366
Evaluate side-chains
  36 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.372 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5193
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6028
moved from start:          0.8390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3516  Z= 0.236
  Angle     :  0.780   9.292   4788  Z= 0.398
  Chirality :  0.060   0.333    606
  Planarity :  0.003   0.023    579
  Dihedral  : 14.516 108.658    711
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.05 %
    Favored  : 98.69 %
  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: -3.93 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS B 239 
   PHE   0.015   0.002   PHE A 237 
   TYR   0.018   0.003   TYR C 125 
   ARG   0.003   0.000   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.373 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0883
  time to fit residues: 5.6421
Evaluate side-chains
  35 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.357 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4644
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6018
moved from start:          0.8509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3516  Z= 0.238
  Angle     :  0.782   9.607   4788  Z= 0.398
  Chirality :  0.059   0.319    606
  Planarity :  0.003   0.026    579
  Dihedral  : 14.256 107.510    711
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -3.91 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS B 239 
   PHE   0.015   0.002   PHE A 237 
   TYR   0.018   0.003   TYR B 143 
   ARG   0.002   0.000   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.391 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0949
  time to fit residues: 5.6480
Evaluate side-chains
  33 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.377 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5294
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 32 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0670
   chunk 12 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    1.5720

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 HIS
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5957
moved from start:          0.8492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3516  Z= 0.213
  Angle     :  0.740   9.682   4788  Z= 0.373
  Chirality :  0.058   0.271    606
  Planarity :  0.003   0.030    579
  Dihedral  : 13.884 107.188    711
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  0.52 %
    Favored  : 98.95 %
  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: -3.76 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS B 239 
   PHE   0.010   0.001   PHE A 237 
   TYR   0.016   0.002   TYR C 250 
   ARG   0.001   0.000   ARG C 140 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.376 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 0.0959
  time to fit residues: 5.9314
Evaluate side-chains
  37 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.374 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0442
  time to fit residues: 0.5966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 ASN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5222 r_free = 0.5222 target = 0.349868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.290195 restraints weight = 13615.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.5523 r_free = 0.5523 target = 0.200151 restraints weight = 3206.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.5523 r_free = 0.5523 target = 0.198922 restraints weight = 9390.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.5127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5127 r_free = 0.5127    target_work(ls_wunit_k1) = 0.312         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5126 r_free = 0.5126    target_work(ls_wunit_k1) = 0.312         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.5126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5841
moved from start:          0.8555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3516  Z= 0.222
  Angle     :  0.751  10.140   4788  Z= 0.382
  Chirality :  0.058   0.277    606
  Planarity :  0.003   0.030    579
  Dihedral  : 13.715 106.558    711
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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: -3.78 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS C 239 
   PHE   0.012   0.002   PHE A 171 
   TYR   0.017   0.002   TYR B 250 
   ARG   0.002   0.000   ARG C 140 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 967.56 seconds
wall clock time: 18 minutes 27.25 seconds (1107.25 seconds total)