Starting phenix.real_space_refine
on Fri Dec  8 12:18:15 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw1_35761/12_2023/8iw1_35761.pdb"
  }
  resolution = 3.4
  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=   0.004 sd=   0.043
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      51      5.16       5
     C    5307      2.51       5
     N    1412      2.21       5
     O    1557      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  206": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  225": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  310": "OD1" <-> "OD2"
    Residue "A PHE  326": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  334": "NH1" <-> "NH2"
    Residue "A TYR  345": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  355": "OD1" <-> "OD2"
    Residue "A ARG  360": "NH1" <-> "NH2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B ASP  312": "OD1" <-> "OD2"
    Residue "B ASP  323": "OD1" <-> "OD2"
    Residue "R PHE   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ASP  112": "OD1" <-> "OD2"
    Residue "R PHE  159": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  163": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  232": "OE1" <-> "OE2"
    Residue "R TYR  274": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  302": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S GLU    6": "OE1" <-> "OE2"
    Residue "S TYR   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S PHE   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S GLU   89": "OE1" <-> "OE2"
    Residue "S PHE  203": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S GLU  220": "OE1" <-> "OE2"
    Residue "S ASP  223": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8327
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1761
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 217}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 45
    Chain: "B"
      Number of atoms: 2483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2483
          Classifications: {'peptide': 333}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "C"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 328
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 43}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "R"
      Number of atoms: 1984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 1984
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 256
          Unresolved non-hydrogen dihedrals: 184
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 128
    Chain: "S"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1771
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 4.69, per 1000 atoms: 0.56
  Number of scatterers: 8327
  At special positions: 0
  Unit cell: (120.7, 93.5, 124.95, 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      51     16.00
     O    1557      8.00
     N    1412      7.00
     C    5307      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03

  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: 3.13
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      33.4% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.646A  pdb=" N   GLN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A  31 " --> pdb=" O   ARG A  27 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 63
      removed outlier: 3.754A  pdb=" N   ILE A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 264
      removed outlier: 3.511A  pdb=" N   ASP A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
      removed outlier: 3.764A  pdb=" N   ARG A 270 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 290
      removed outlier: 4.035A  pdb=" N   GLU A 286 " --> pdb=" O   ASP A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 3.711A  pdb=" N   ILE A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 365
      removed outlier: 4.402A  pdb=" N   ARG A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 378
    Processing helix  chain 'B' and resid 9 through 26
      removed outlier: 3.552A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 36
      removed outlier: 3.584A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 32 through 36'
    Processing helix  chain 'C' and resid 17 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.673A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'R' and resid 33 through 38
      removed outlier: 4.472A  pdb=" N   GLY R  37 " --> pdb=" O   ALA R  33 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL R  38 " --> pdb=" O   ILE R  34 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 33 through 38'
    Processing helix  chain 'R' and resid 42 through 48
    Processing helix  chain 'R' and resid 50 through 59
      removed outlier: 3.979A  pdb=" N   ILE R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 96
      removed outlier: 3.509A  pdb=" N   PHE R  69 " --> pdb=" O   THR R  65 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU R  70 " --> pdb=" O   PRO R  66 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA R  72 " --> pdb=" O   ASN R  68 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU R  74 " --> pdb=" O   LEU R  70 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      Proline residue:  R  87  - end of helix
      removed outlier: 4.773A  pdb=" N   VAL R  91 " --> pdb=" O   PRO R  87 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ARG R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 135
      removed outlier: 4.209A  pdb=" N   CYS R 105 " --> pdb=" O   GLY R 101 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LYS R 106 " --> pdb=" O   GLU R 102 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   PHE R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR R 113 " --> pdb=" O   THR R 109 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER R 114 " --> pdb=" O   CYS R 110 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   PHE R 117 " --> pdb=" O   THR R 113 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   CYS R 124 " --> pdb=" O   LEU R 120 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   CYS R 125 " --> pdb=" O   PHE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 168
    Processing helix  chain 'R' and resid 198 through 226
      removed outlier: 3.590A  pdb=" N   PHE R 206 " --> pdb=" O   CYS R 202 " (cutoff:3.500A)
      Proline residue:  R 209  - end of helix
      removed outlier: 3.684A  pdb=" N   TYR R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 254 through 284
      removed outlier: 3.801A  pdb=" N   ALA R 263 " --> pdb=" O   THR R 259 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 291 through 304
      removed outlier: 4.670A  pdb=" N   ILE R 295 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL R 297 " --> pdb=" O   TYR R 293 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL R 300 " --> pdb=" O   LEU R 296 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   SER R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 311
      removed outlier: 4.033A  pdb=" N   TYR R 311 " --> pdb=" O   ASN R 307 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 315 through 327
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.739A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 197
    Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197
      removed outlier: 6.767A  pdb=" N   HIS A  43 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   PHE A 209 " --> pdb=" O   HIS A  43 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ARG A  44 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   ILE A 232 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   LEU A  46 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ILE A 231 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   PHE A 277 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TYR A 233 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ASN A 279 " --> pdb=" O   TYR A 233 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA A 235 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.822A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.617A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.230A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.598A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.814A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.687A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.790A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.790A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG S  98 " --> pdb=" O   PHE S 110 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.091A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    1011 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: 2.98

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1349
        1.29 -     1.42: 2320
        1.42 -     1.55: 4765
        1.55 -     1.68: 5
        1.68 -     1.81: 72
  Bond restraints: 8511
  Sorted by residual:
  bond pdb=" C   LEU S 178 "
       pdb=" O   LEU S 178 "
    ideal  model  delta    sigma   weight residual
    1.235  1.156  0.079 1.13e-02 7.83e+03 4.93e+01
  bond pdb=" C   TYR R 226 "
       pdb=" O   TYR R 226 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.33e-02 5.65e+03 2.72e+01
  bond pdb=" C   LYS R 230 "
       pdb=" O   LYS R 230 "
    ideal  model  delta    sigma   weight residual
    1.237  1.175  0.061 1.19e-02 7.06e+03 2.65e+01
  bond pdb=" CA  ASP A 258 "
       pdb=" C   ASP A 258 "
    ideal  model  delta    sigma   weight residual
    1.524  1.459  0.064 1.26e-02 6.30e+03 2.62e+01
  bond pdb=" CA  LEU A  28 "
       pdb=" C   LEU A  28 "
    ideal  model  delta    sigma   weight residual
    1.524  1.462  0.062 1.24e-02 6.50e+03 2.50e+01
  ... (remaining 8506 not shown)

  Histogram of bond angle deviations from ideal:
       99.70 -   106.56: 208
      106.56 -   113.43: 4587
      113.43 -   120.30: 3110
      120.30 -   127.16: 3589
      127.16 -   134.03: 91
  Bond angle restraints: 11585
  Sorted by residual:
  angle pdb=" N   THR A 356 "
        pdb=" CA  THR A 356 "
        pdb=" C   THR A 356 "
      ideal   model   delta    sigma   weight residual
     110.97  119.90   -8.93 1.09e+00 8.42e-01 6.71e+01
  angle pdb=" N   ASN A 358 "
        pdb=" CA  ASN A 358 "
        pdb=" C   ASN A 358 "
      ideal   model   delta    sigma   weight residual
     112.59  103.36    9.23 1.22e+00 6.72e-01 5.73e+01
  angle pdb=" N   VAL A 354 "
        pdb=" CA  VAL A 354 "
        pdb=" C   VAL A 354 "
      ideal   model   delta    sigma   weight residual
     110.62  118.32   -7.70 1.02e+00 9.61e-01 5.70e+01
  angle pdb=" N   HIS R  59 "
        pdb=" CA  HIS R  59 "
        pdb=" C   HIS R  59 "
      ideal   model   delta    sigma   weight residual
     111.14  118.12   -6.98 1.08e+00 8.57e-01 4.18e+01
  angle pdb=" N   LEU A  28 "
        pdb=" CA  LEU A  28 "
        pdb=" C   LEU A  28 "
      ideal   model   delta    sigma   weight residual
     111.03  103.87    7.16 1.11e+00 8.12e-01 4.16e+01
  ... (remaining 11580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 4321
       16.80 -    33.59: 496
       33.59 -    50.39: 129
       50.39 -    67.18: 19
       67.18 -    83.98: 10
  Dihedral angle restraints: 4975
    sinusoidal: 1762
      harmonic: 3213
  Sorted by residual:
  dihedral pdb=" CA  CYS A 366 "
           pdb=" C   CYS A 366 "
           pdb=" N   ARG A 367 "
           pdb=" CA  ARG A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  GLN R 227 "
           pdb=" C   GLN R 227 "
           pdb=" N   ALA R 228 "
           pdb=" CA  ALA R 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.08   20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" C   PHE R  60 "
           pdb=" N   PHE R  60 "
           pdb=" CA  PHE R  60 "
           pdb=" CB  PHE R  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.80   10.20     0      2.50e+00 1.60e-01 1.66e+01
  ... (remaining 4972 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1250
       0.103 -    0.205: 62
       0.205 -    0.307: 12
       0.307 -    0.410: 4
       0.410 -    0.512: 5
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" CA  TYR R 226 "
            pdb=" N   TYR R 226 "
            pdb=" C   TYR R 226 "
            pdb=" CB  TYR R 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.56e+00
  chirality pdb=" CA  PHE R  60 "
            pdb=" N   PHE R  60 "
            pdb=" C   PHE R  60 "
            pdb=" CB  PHE R  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.95e+00
  chirality pdb=" CA  PHE R 207 "
            pdb=" N   PHE R 207 "
            pdb=" C   PHE R 207 "
            pdb=" CB  PHE R 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.97e+00
  ... (remaining 1330 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 352 "   -0.020 2.00e-02 2.50e+03   3.94e-02 1.55e+01
        pdb=" C   CYS A 352 "    0.068 2.00e-02 2.50e+03
        pdb=" O   CYS A 352 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA A 353 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 257 "   -0.013 2.00e-02 2.50e+03   2.77e-02 7.70e+00
        pdb=" C   LEU A 257 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LEU A 257 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ASP A 258 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 260 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.69e+00
        pdb=" C   PHE A 260 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE A 260 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLU A 261 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 516
        2.72 -     3.27: 8090
        3.27 -     3.81: 12826
        3.81 -     4.36: 15138
        4.36 -     4.90: 26997
  Nonbonded interactions: 63567
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  15 "
            pdb=" O   VAL B  90 "
     model   vdw
     2.179 2.520
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.180 2.440
  nonbonded pdb=" O   CYS R 110 "
            pdb=" OG  SER R 164 "
     model   vdw
     2.203 2.440
  nonbonded pdb=" O   SER S  52 "
            pdb=" NH1 ARG S  72 "
     model   vdw
     2.224 2.520
  nonbonded pdb=" NE1 TRP S  47 "
            pdb=" O   ALA S  49 "
     model   vdw
     2.244 2.520
  ... (remaining 63562 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          2.120
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.120
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:3.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
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      :  0.007   0.079   8511  Z= 0.453
  Angle     :  0.860  12.572  11585  Z= 0.558
  Chirality :  0.063   0.512   1333
  Planarity :  0.005   0.048   1472
  Dihedral  : 15.677  83.981   2897
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 15.13 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.25), residues: 1085
  helix: -0.67 (0.29), residues: 343
  sheet: -0.51 (0.32), residues: 267
  loop : -1.98 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP R 271 
   HIS   0.008   0.001   HIS R  59 
   PHE   0.026   0.002   PHE R  60 
   TYR   0.024   0.002   TYR S 235 
   ARG   0.007   0.000   ARG B 129 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 187
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 190
  average time/residue: 0.2384
  time to fit residues: 58.6894
Evaluate side-chains
  159 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.898 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0767
  time to fit residues: 1.5371
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0870
   chunk 45 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
A 358 ASN
A 377 GLN
B 176 GLN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8511  Z= 0.167
  Angle     :  0.549   7.058  11585  Z= 0.293
  Chirality :  0.041   0.177   1333
  Planarity :  0.004   0.040   1472
  Dihedral  :  4.527  20.199   1191
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.32 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.25), residues: 1085
  helix:  0.16 (0.29), residues: 345
  sheet: -0.33 (0.32), residues: 273
  loop : -1.90 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 169 
   HIS   0.004   0.001   HIS R  64 
   PHE   0.014   0.001   PHE B 234 
   TYR   0.023   0.001   TYR S 235 
   ARG   0.007   0.001   ARG A 361 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 17
  residues processed: 172
  average time/residue: 0.2772
  time to fit residues: 62.1666
Evaluate side-chains
  170 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0812
  time to fit residues: 3.7765
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 107 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 303 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8511  Z= 0.172
  Angle     :  0.526   6.355  11585  Z= 0.277
  Chirality :  0.041   0.175   1333
  Planarity :  0.004   0.052   1472
  Dihedral  :  4.330  18.376   1191
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 21.75 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1085
  helix:  0.74 (0.30), residues: 342
  sheet:  0.05 (0.33), residues: 258
  loop : -1.83 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  99 
   HIS   0.005   0.001   HIS R 122 
   PHE   0.029   0.001   PHE A 225 
   TYR   0.021   0.001   TYR S 235 
   ARG   0.009   0.001   ARG S  67 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 5
  residues processed: 171
  average time/residue: 0.2493
  time to fit residues: 55.6877
Evaluate side-chains
  158 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 153
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0790
  time to fit residues: 1.9642
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 99 optimal weight:    9.9990
   chunk 105 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  44 HIS
R 303 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   8511  Z= 0.425
  Angle     :  0.698   8.638  11585  Z= 0.369
  Chirality :  0.047   0.214   1333
  Planarity :  0.005   0.052   1472
  Dihedral  :  5.043  24.942   1191
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 22.93 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.25), residues: 1085
  helix:  0.24 (0.29), residues: 355
  sheet:  0.12 (0.34), residues: 246
  loop : -1.91 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.003   TRP B 169 
   HIS   0.012   0.002   HIS R 122 
   PHE   0.032   0.003   PHE S  29 
   TYR   0.037   0.003   TYR S  59 
   ARG   0.009   0.001   ARG B  68 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 33
  outliers final: 19
  residues processed: 178
  average time/residue: 0.2433
  time to fit residues: 56.6524
Evaluate side-chains
  174 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.826 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0918
  time to fit residues: 4.1606
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
B 340 ASN
R 303 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8511  Z= 0.223
  Angle     :  0.580   8.876  11585  Z= 0.303
  Chirality :  0.042   0.195   1333
  Planarity :  0.004   0.047   1472
  Dihedral  :  4.653  21.985   1191
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 23.52 %
    Favored  : 74.23 %
  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: -0.87 (0.25), residues: 1085
  helix:  0.57 (0.29), residues: 348
  sheet:  0.07 (0.32), residues: 269
  loop : -1.88 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B 169 
   HIS   0.005   0.001   HIS S  35 
   PHE   0.013   0.001   PHE S  29 
   TYR   0.025   0.002   TYR S 235 
   ARG   0.007   0.001   ARG B  68 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 8
  residues processed: 173
  average time/residue: 0.2385
  time to fit residues: 55.1946
Evaluate side-chains
  161 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 0.916 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0788
  time to fit residues: 2.4571
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
B  75 GLN
B 268 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8511  Z= 0.355
  Angle     :  0.646   9.635  11585  Z= 0.339
  Chirality :  0.045   0.203   1333
  Planarity :  0.005   0.052   1472
  Dihedral  :  4.921  23.530   1191
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 25.30 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1085
  helix:  0.52 (0.29), residues: 345
  sheet:  0.11 (0.32), residues: 272
  loop : -1.85 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B 169 
   HIS   0.009   0.002   HIS S  35 
   PHE   0.022   0.002   PHE S  29 
   TYR   0.032   0.002   TYR S  59 
   ARG   0.007   0.001   ARG B 219 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 16
  residues processed: 175
  average time/residue: 0.2252
  time to fit residues: 52.7188
Evaluate side-chains
  174 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.878 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0807
  time to fit residues: 3.6236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 105 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0980
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
B  75 GLN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8511  Z= 0.226
  Angle     :  0.579   9.415  11585  Z= 0.300
  Chirality :  0.043   0.187   1333
  Planarity :  0.004   0.047   1472
  Dihedral  :  4.638  21.420   1191
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 25.77 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.25), residues: 1085
  helix:  0.70 (0.30), residues: 346
  sheet:  0.20 (0.32), residues: 266
  loop : -1.82 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B 169 
   HIS   0.006   0.001   HIS S  35 
   PHE   0.013   0.001   PHE S  29 
   TYR   0.023   0.002   TYR S 235 
   ARG   0.008   0.001   ARG A 267 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 162
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 166
  average time/residue: 0.2262
  time to fit residues: 50.6468
Evaluate side-chains
  163 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 158
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0800
  time to fit residues: 1.9825
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8511  Z= 0.213
  Angle     :  0.565   9.380  11585  Z= 0.292
  Chirality :  0.042   0.181   1333
  Planarity :  0.004   0.046   1472
  Dihedral  :  4.532  20.561   1191
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 26.71 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.26), residues: 1085
  helix:  0.86 (0.30), residues: 346
  sheet:  0.18 (0.32), residues: 271
  loop : -1.72 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B 169 
   HIS   0.006   0.001   HIS S  35 
   PHE   0.013   0.001   PHE S  29 
   TYR   0.022   0.002   TYR S 235 
   ARG   0.008   0.000   ARG A 267 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 8
  residues processed: 161
  average time/residue: 0.2335
  time to fit residues: 50.2858
Evaluate side-chains
  160 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.901 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0823
  time to fit residues: 2.4629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0020
   chunk 64 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
B  75 GLN
B 110 ASN
** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8511  Z= 0.147
  Angle     :  0.533   9.097  11585  Z= 0.271
  Chirality :  0.041   0.177   1333
  Planarity :  0.004   0.044   1472
  Dihedral  :  4.264  18.107   1191
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 26.83 %
    Favored  : 72.34 %
  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: -0.34 (0.26), residues: 1085
  helix:  1.08 (0.30), residues: 349
  sheet:  0.45 (0.33), residues: 261
  loop : -1.67 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP R 317 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.012   0.001   PHE R 206 
   TYR   0.020   0.001   TYR S 235 
   ARG   0.008   0.001   ARG A 267 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.893 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 162
  average time/residue: 0.2210
  time to fit residues: 48.0877
Evaluate side-chains
  158 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.891 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1724
  time to fit residues: 2.0682
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 108 optimal weight:    0.1980
   chunk 99 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0060
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    0.2980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
B 110 ASN
R 307 ASN
S 231 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8511  Z= 0.134
  Angle     :  0.519   8.753  11585  Z= 0.263
  Chirality :  0.041   0.170   1333
  Planarity :  0.004   0.043   1472
  Dihedral  :  4.058  18.107   1191
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 27.42 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1085
  helix:  1.37 (0.30), residues: 349
  sheet:  0.42 (0.32), residues: 267
  loop : -1.56 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP R 317 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.012   0.001   PHE R 206 
   TYR   0.017   0.001   TYR S 235 
   ARG   0.008   0.000   ARG A 267 

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 0.808 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 150
  average time/residue: 0.2355
  time to fit residues: 46.9386
Evaluate side-chains
  143 residues out of total 943 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0801
  time to fit residues: 1.4053
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0060
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
** S 231 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.135678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117419 restraints weight = 12409.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.13
r_work: 0.3434 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8511  Z= 0.145
  Angle     :  0.520   9.055  11585  Z= 0.263
  Chirality :  0.041   0.171   1333
  Planarity :  0.003   0.043   1472
  Dihedral  :  4.050  18.022   1191
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 28.37 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1085
  helix:  1.46 (0.30), residues: 349
  sheet:  0.52 (0.32), residues: 266
  loop : -1.52 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP R 317 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.011   0.001   PHE R 206 
   TYR   0.017   0.001   TYR S 235 
   ARG   0.008   0.000   ARG R  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2198.99 seconds
wall clock time: 40 minutes 18.11 seconds (2418.11 seconds total)