Starting phenix.real_space_refine
on Fri Jul 19 15:57:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g59_29736/07_2024/8g59_29736.cif"
  }
  resolution = 2.64
  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=   0.008 sd=   0.088
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      58      5.16       5
     C    5503      2.51       5
     N    1444      2.21       5
     O    1577      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 8583
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2509
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "Y"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "S"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1739
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1739
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2204
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
      Conformer: "B"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
          bond proxies already assigned to first conformer: 2231
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'YN9': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE R 115 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 115 " occ=0.50
  Time building chain proxies: 6.73, per 1000 atoms: 0.78
  Number of scatterers: 8583
  At special positions: 0
  Unit cell: (105.456, 121.68, 115.596, 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      58     16.00
     F       1      9.00
     O    1577      8.00
     N    1444      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " 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
  Time building additional restraints: 3.57
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      37.4% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'Y' and resid 10 through 24
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'Y' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.619A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.985A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.388A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.367A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.940A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 335 through 355
    Processing helix  chain 'R' and resid 42 through 70
    Processing helix  chain 'R' and resid 78 through 91
      removed outlier: 3.956A  pdb=" N   ALA R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 101
      removed outlier: 3.628A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 142
      removed outlier: 4.695A  pdb=" N  APHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 169
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.658A  pdb=" N   PHE R 176 " --> pdb=" O   PRO R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 244
      removed outlier: 3.556A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL R 209 " --> pdb=" O   ILE R 205 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   VAL R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      Proline residue:  R 219  - end of helix
      removed outlier: 3.958A  pdb=" N   ARG R 238 " --> pdb=" O   THR R 234 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 292
      removed outlier: 3.614A  pdb=" N   LEU R 262 " --> pdb=" O   GLN R 258 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE R 263 " --> pdb=" O   ASP R 259 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 299 through 321
      removed outlier: 3.903A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.541A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.627A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.826A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.484A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.593A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.714A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.527A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS S  22 " --> pdb=" O   LEU S  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.572A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.559A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.624A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.697A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 9.010A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 177 through 182

    437 hydrogen bonds defined for protein.
    1231 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: 2.46

  Time building geometry restraints manager: 3.95 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1365
        1.26 -     1.40: 2177
        1.40 -     1.53: 4857
        1.53 -     1.67: 280
        1.67 -     1.81: 84
  Bond restraints: 8763
  Sorted by residual:
  bond pdb=" C   PHE R 260 "
       pdb=" O   PHE R 260 "
    ideal  model  delta    sigma   weight residual
    1.233  1.117  0.116 1.46e-02 4.69e+03 6.29e+01
  bond pdb=" N   GLN R 258 "
       pdb=" CA  GLN R 258 "
    ideal  model  delta    sigma   weight residual
    1.458  1.383  0.074 1.33e-02 5.65e+03 3.12e+01
  bond pdb=" N   ASP R 259 "
       pdb=" CA  ASP R 259 "
    ideal  model  delta    sigma   weight residual
    1.456  1.393  0.063 1.18e-02 7.18e+03 2.84e+01
  bond pdb=" C   ARG R  36 "
       pdb=" O   ARG R  36 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.063 1.25e-02 6.40e+03 2.54e+01
  bond pdb=" C1  YN9 R 401 "
       pdb=" C3  YN9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.481  1.581 -0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 8758 not shown)

  Histogram of bond angle deviations from ideal:
      100.24 -   107.00: 206
      107.00 -   113.77: 4920
      113.77 -   120.53: 3309
      120.53 -   127.30: 3385
      127.30 -   134.06: 90
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   PHE R 260 "
        pdb=" CA  PHE R 260 "
        pdb=" C   PHE R 260 "
      ideal   model   delta    sigma   weight residual
     114.04  102.67   11.37 1.24e+00 6.50e-01 8.41e+01
  angle pdb=" C   ALA R  91 "
        pdb=" N   ILE R  92 "
        pdb=" CA  ILE R  92 "
      ideal   model   delta    sigma   weight residual
     120.24  124.87   -4.63 6.30e-01 2.52e+00 5.39e+01
  angle pdb=" N   ILE R  89 "
        pdb=" CA  ILE R  89 "
        pdb=" C   ILE R  89 "
      ideal   model   delta    sigma   weight residual
     110.62  117.17   -6.55 1.02e+00 9.61e-01 4.13e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  118.33   -6.97 1.09e+00 8.42e-01 4.09e+01
  angle pdb=" C   ASP R 259 "
        pdb=" CA  ASP R 259 "
        pdb=" CB  ASP R 259 "
      ideal   model   delta    sigma   weight residual
     110.94  120.06   -9.12 1.65e+00 3.67e-01 3.05e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 4695
       15.94 -    31.87: 364
       31.87 -    47.81: 62
       47.81 -    63.75: 16
       63.75 -    79.68: 7
  Dihedral angle restraints: 5144
    sinusoidal: 1900
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" C   ASP R 259 "
           pdb=" N   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.58   21.98     0      2.50e+00 1.60e-01 7.73e+01
  dihedral pdb=" N   ASP R 259 "
           pdb=" C   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.49  -19.69     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" CB  CYS R 111 "
           pdb=" SG  CYS R 111 "
           pdb=" SG  CYS R 194 "
           pdb=" CB  CYS R 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.64   65.36     1      1.00e+01 1.00e-02 5.60e+01
  ... (remaining 5141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 1389
       0.197 -    0.394: 3
       0.394 -    0.591: 0
       0.591 -    0.788: 0
       0.788 -    0.985: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASP R 259 "
            pdb=" N   ASP R 259 "
            pdb=" C   ASP R 259 "
            pdb=" CB  ASP R 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.53    0.99 2.00e-01 2.50e+01 2.43e+01
  chirality pdb=" CA  ARG R 254 "
            pdb=" N   ARG R 254 "
            pdb=" C   ARG R 254 "
            pdb=" CB  ARG R 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  GLN R 258 "
            pdb=" N   GLN R 258 "
            pdb=" C   GLN R 258 "
            pdb=" CB  GLN R 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 257 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.19e+01
        pdb=" C   GLN R 257 "    0.098 2.00e-02 2.50e+03
        pdb=" O   GLN R 257 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLN R 258 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.075 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO S  75 "    0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R 299 "    0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO R 300 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1488 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 57
        2.52 -     3.12: 6315
        3.12 -     3.71: 13279
        3.71 -     4.31: 19213
        4.31 -     4.90: 32205
  Nonbonded interactions: 71069
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG R 238 "
            pdb=" OD2 ASP R 259 "
     model   vdw
     1.930 2.520
  nonbonded pdb=" O   CYS R  60 "
            pdb=" CD2 LEU R  64 "
     model   vdw
     1.953 3.460
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.183 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.222 2.440
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.255 2.520
  ... (remaining 71064 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     29.170
  Find NCS groups from input model:        0.090
  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:11.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116   8763  Z= 0.334
  Angle     :  0.728  11.682  11910  Z= 0.430
  Chirality :  0.053   0.985   1393
  Planarity :  0.006   0.112   1491
  Dihedral  : 12.160  79.684   3036
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.88 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 1095
  helix:  0.23 (0.25), residues: 387
  sheet:  0.39 (0.30), residues: 301
  loop : -0.65 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 251 
 PHE   0.016   0.001   PHE R 311 
 TYR   0.017   0.001   TYR A 302 
 ARG   0.007   0.000   ARG R  36 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 LYS cc_start: 0.9253 (mttm) cc_final: 0.9006 (mttp)
REVERT: R  165 TYR cc_start: 0.7006 (t80) cc_final: 0.6178 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 1.4875
  time to fit residues: 251.9597
Evaluate side-chains
  135 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0000
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.4384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S 186 GLN
A 357 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8763  Z= 0.167
  Angle     :  0.591  10.693  11910  Z= 0.300
  Chirality :  0.042   0.134   1393
  Planarity :  0.005   0.074   1491
  Dihedral  :  4.987  55.249   1208
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.57 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1095
  helix:  1.27 (0.27), residues: 373
  sheet:  0.53 (0.31), residues: 297
  loop : -0.32 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.007   0.001   ARG B 129 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  335 PHE cc_start: 0.8661 (m-80) cc_final: 0.8432 (m-80)
REVERT: A  193 ASP cc_start: 0.7962 (p0) cc_final: 0.7751 (p0)
REVERT: R  165 TYR cc_start: 0.6977 (t80) cc_final: 0.5923 (t80)
REVERT: R  240 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5598 (ptt90)
  outliers start: 10
  outliers final: 3
  residues processed: 148
  average time/residue: 1.3813
  time to fit residues: 215.9507
Evaluate side-chains
  126 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0070
   chunk 68 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 34 optimal weight:   20.0000
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.9804

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN
S 194 ASN
A 188 HIS
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8763  Z= 0.200
  Angle     :  0.566  10.562  11910  Z= 0.288
  Chirality :  0.042   0.132   1393
  Planarity :  0.005   0.062   1491
  Dihedral  :  4.497  41.952   1206
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.56 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.26), residues: 1095
  helix:  1.26 (0.27), residues: 383
  sheet:  0.74 (0.31), residues: 284
  loop : -0.36 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 104 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.011   0.001   PHE R 304 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.011   0.001   ARG R 261 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8149 (mptm)
REVERT: A  240 MET cc_start: 0.6647 (ptt) cc_final: 0.6278 (ptp)
REVERT: A  346 ASP cc_start: 0.5760 (m-30) cc_final: 0.4917 (t70)
REVERT: R  165 TYR cc_start: 0.7037 (t80) cc_final: 0.5926 (t80)
  outliers start: 18
  outliers final: 7
  residues processed: 140
  average time/residue: 1.5247
  time to fit residues: 224.8203
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain R residue   49 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 67 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 95 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8763  Z= 0.178
  Angle     :  0.558  10.614  11910  Z= 0.282
  Chirality :  0.041   0.136   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.387  40.528   1206
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.54 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1095
  helix:  1.48 (0.27), residues: 382
  sheet:  0.59 (0.31), residues: 294
  loop : -0.28 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.011   0.001   ARG R 261 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.7903 (p0) cc_final: 0.7558 (p0)
REVERT: A  193 ASP cc_start: 0.7968 (p0) cc_final: 0.7716 (p0)
REVERT: A  240 MET cc_start: 0.6655 (ptt) cc_final: 0.6314 (ptp)
REVERT: A  247 MET cc_start: 0.8378 (mtm) cc_final: 0.8164 (ttm)
REVERT: A  248 LYS cc_start: 0.8533 (mppt) cc_final: 0.8246 (mtmm)
REVERT: R  165 TYR cc_start: 0.7083 (t80) cc_final: 0.5966 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 147
  average time/residue: 1.3983
  time to fit residues: 217.1670
Evaluate side-chains
  136 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain R residue   49 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 54 optimal weight:    5.9990
   chunk 95 optimal weight:    0.4980
   chunk 26 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
Y  59 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8763  Z= 0.174
  Angle     :  0.549  11.105  11910  Z= 0.278
  Chirality :  0.041   0.137   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.325  39.802   1206
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.97 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1095
  helix:  1.68 (0.27), residues: 378
  sheet:  0.62 (0.31), residues: 294
  loop : -0.26 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.021   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.014   0.001   ARG R 261 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7407 (mtp85)
REVERT: A  240 MET cc_start: 0.6599 (ptt) cc_final: 0.6332 (ptp)
REVERT: A  283 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8287 (tt)
REVERT: A  346 ASP cc_start: 0.5878 (m-30) cc_final: 0.4934 (t70)
REVERT: R  165 TYR cc_start: 0.7093 (t80) cc_final: 0.5952 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 146
  average time/residue: 1.5084
  time to fit residues: 231.7448
Evaluate side-chains
  142 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain R residue   49 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0970
   chunk 8 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0870
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8763  Z= 0.172
  Angle     :  0.548  11.462  11910  Z= 0.277
  Chirality :  0.041   0.137   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.213  37.219   1206
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.74 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.03 (0.26), residues: 1095
  helix:  1.77 (0.27), residues: 383
  sheet:  0.62 (0.30), residues: 294
  loop : -0.20 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.020   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG R 254 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7376 (mtp85)
REVERT: A  193 ASP cc_start: 0.7950 (p0) cc_final: 0.7727 (p0)
REVERT: A  240 MET cc_start: 0.6666 (ptt) cc_final: 0.6420 (ptp)
REVERT: R  165 TYR cc_start: 0.7115 (t80) cc_final: 0.5966 (t80)
REVERT: R  240 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6096 (ptp90)
  outliers start: 19
  outliers final: 9
  residues processed: 152
  average time/residue: 1.4601
  time to fit residues: 233.6774
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8763  Z= 0.367
  Angle     :  0.639  11.746  11910  Z= 0.323
  Chirality :  0.045   0.156   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.672  41.681   1206
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.95 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1095
  helix:  1.21 (0.27), residues: 383
  sheet:  0.70 (0.30), residues: 292
  loop : -0.25 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.016   0.002   PHE R 177 
 TYR   0.010   0.002   TYR S 103 
 ARG   0.009   0.001   ARG B 129 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7457 (mtp85)
REVERT: B   78 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8136 (mptm)
REVERT: A  193 ASP cc_start: 0.7973 (p0) cc_final: 0.7756 (p0)
REVERT: A  248 LYS cc_start: 0.8545 (mppt) cc_final: 0.8268 (mtmm)
REVERT: R  165 TYR cc_start: 0.7247 (t80) cc_final: 0.7038 (t80)
REVERT: R  240 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6121 (ptp90)
  outliers start: 17
  outliers final: 11
  residues processed: 149
  average time/residue: 1.4530
  time to fit residues: 228.1361
Evaluate side-chains
  144 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
Y  59 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8763  Z= 0.210
  Angle     :  0.576   8.379  11910  Z= 0.293
  Chirality :  0.042   0.145   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.393  34.304   1206
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.84 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1095
  helix:  1.45 (0.27), residues: 388
  sheet:  0.68 (0.31), residues: 292
  loop : -0.24 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.019   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.012   0.001   ARG S 202 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7460 (mtp85)
REVERT: A  248 LYS cc_start: 0.8537 (mppt) cc_final: 0.8280 (mtmm)
REVERT: A  346 ASP cc_start: 0.5980 (m-30) cc_final: 0.4977 (t70)
REVERT: R  165 TYR cc_start: 0.7169 (t80) cc_final: 0.6028 (t80)
REVERT: R  240 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6252 (ptp90)
  outliers start: 19
  outliers final: 11
  residues processed: 145
  average time/residue: 1.5122
  time to fit residues: 230.7869
Evaluate side-chains
  145 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.0010
   chunk 101 optimal weight:    0.5980
   chunk 59 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
A 204 GLN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8763  Z= 0.169
  Angle     :  0.574  11.949  11910  Z= 0.288
  Chirality :  0.041   0.142   1393
  Planarity :  0.005   0.064   1491
  Dihedral  :  4.228  30.279   1206
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.50 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.03 (0.26), residues: 1095
  helix:  1.73 (0.27), residues: 383
  sheet:  0.66 (0.31), residues: 294
  loop : -0.20 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.014   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.012   0.001   ARG S 202 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7406 (mtp85)
REVERT: A  240 MET cc_start: 0.5655 (ptp) cc_final: 0.4914 (ttm)
REVERT: A  248 LYS cc_start: 0.8509 (mppt) cc_final: 0.8262 (mtmm)
REVERT: A  346 ASP cc_start: 0.5927 (m-30) cc_final: 0.4903 (t70)
REVERT: R  165 TYR cc_start: 0.7121 (t80) cc_final: 0.5949 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 145
  average time/residue: 1.4522
  time to fit residues: 221.9751
Evaluate side-chains
  147 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  333 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 109 optimal weight:    0.1980
   chunk 100 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
Y  59 ASN
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8763  Z= 0.247
  Angle     :  0.606  11.885  11910  Z= 0.305
  Chirality :  0.042   0.153   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.376  31.366   1206
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.50 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1095
  helix:  1.50 (0.27), residues: 389
  sheet:  0.68 (0.30), residues: 292
  loop : -0.22 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 104 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.020   0.002   PHE R 263 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.011   0.001   ARG S 202 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7439 (mtp85)
REVERT: B   78 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8138 (mptm)
REVERT: A  193 ASP cc_start: 0.7955 (p0) cc_final: 0.7754 (p0)
REVERT: A  240 MET cc_start: 0.5688 (ptp) cc_final: 0.5043 (ttm)
REVERT: R  165 TYR cc_start: 0.7201 (t80) cc_final: 0.5994 (t80)
REVERT: R  178 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6202 (mmp80)
REVERT: R  240 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6128 (ptp90)
  outliers start: 17
  outliers final: 8
  residues processed: 148
  average time/residue: 1.4622
  time to fit residues: 228.0751
Evaluate side-chains
  149 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0670
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 268 ASN
** Y  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.156065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.121892 restraints weight = 20539.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.44
r_work: 0.3564 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8763  Z= 0.199
  Angle     :  0.580   9.018  11910  Z= 0.294
  Chirality :  0.042   0.146   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.265  29.370   1206
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.94 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1095
  helix:  1.67 (0.27), residues: 384
  sheet:  0.67 (0.31), residues: 289
  loop : -0.23 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.013   0.001   PHE R 260 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.011   0.001   ARG S 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4290.50 seconds
wall clock time: 75 minutes 31.72 seconds (4531.72 seconds total)