Starting phenix.real_space_refine
on Fri Dec  8 17:26:23 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vl8_32020/12_2023/7vl8_32020_updated.pdb"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      58      5.16       5
     C    5681      2.51       5
     N    1495      2.21       5
     O    1600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A ARG  208": "NH1" <-> "NH2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "A GLU  276": "OE1" <-> "OE2"
    Residue "B GLU    3": "OE1" <-> "OE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B ARG   22": "NH1" <-> "NH2"
    Residue "B ARG   42": "NH1" <-> "NH2"
    Residue "B ARG   49": "NH1" <-> "NH2"
    Residue "B ARG  197": "NH1" <-> "NH2"
    Residue "B GLU  215": "OE1" <-> "OE2"
    Residue "B ARG  314": "NH1" <-> "NH2"
    Residue "G GLU   17": "OE1" <-> "OE2"
    Residue "S ARG   98": "NH1" <-> "NH2"
    Residue "S ARG  160": "NH1" <-> "NH2"
    Residue "S ARG  218": "NH1" <-> "NH2"
    Residue "S GLU  222": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8834
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1666
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2593
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2358
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 9, 'TRANS': 274}
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1751
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.96, per 1000 atoms: 0.56
  Number of scatterers: 8834
  At special positions: 0
  Unit cell: (111.54, 133.848, 116.61, 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      58     16.00
     O    1600      8.00
     N    1495      7.00
     C    5681      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " 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: 3.47
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      34.5% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.616A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 208 through 211
      No H-bonds generated for 'chain 'A' and resid 208 through 211'
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 227 through 230
      removed outlier: 3.931A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 227 through 230'
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 277
      removed outlier: 4.132A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.911A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.840A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.982A  pdb=" N   LEU R  40 " --> pdb=" O   LEU R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 96
      removed outlier: 3.895A  pdb=" N   THR R  86 " --> pdb=" O   LEU R  82 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LEU R  87 " --> pdb=" O   PHE R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 103 through 135
      removed outlier: 3.802A  pdb=" N   GLY R 111 " --> pdb=" O   LYS R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 144
    Processing helix  chain 'R' and resid 147 through 164
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 189 through 205
      removed outlier: 5.462A  pdb=" N   ARG R 193 " --> pdb=" O   GLU R 190 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU R 197 " --> pdb=" O   GLU R 194 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN R 199 " --> pdb=" O   LYS R 196 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU R 205 " --> pdb=" O   LYS R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 226
      removed outlier: 4.069A  pdb=" N   ILE R 225 " --> pdb=" O   GLY R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 268
      Proline residue:  R 254  - end of helix
      removed outlier: 3.508A  pdb=" N   GLN R 265 " --> pdb=" O   ILE R 261 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   ASP R 266 " --> pdb=" O   SER R 262 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   PHE R 267 " --> pdb=" O   VAL R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 301
      removed outlier: 4.342A  pdb=" N   LEU R 281 " --> pdb=" O   ARG R 277 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
      removed outlier: 3.619A  pdb=" N   HIS R 317 " --> pdb=" O   ARG R 313 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.388A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.832A  pdb=" N   GLY A  40 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.864A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.978A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.724A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.005A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.615A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.648A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 317 through 320
      removed outlier: 3.880A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'R' and resid 172 through 176
      removed outlier: 3.697A  pdb=" N   SER R 184 " --> pdb=" O   LYS R 173 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.170A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.737A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=  N, first strand: chain 'S' and resid 229 through 231
      removed outlier: 6.485A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1116 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: 2.80

  Time building geometry restraints manager: 3.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1563
        1.32 -     1.45: 2420
        1.45 -     1.57: 4962
        1.57 -     1.69: 3
        1.69 -     1.81: 83
  Bond restraints: 9031
  Sorted by residual:
  bond pdb=" NE  ARG R 143 "
       pdb=" CZ  ARG R 143 "
    ideal  model  delta    sigma   weight residual
    1.326  1.365 -0.039 1.10e-02 8.26e+03 1.29e+01
  bond pdb=" CB  LEU R  65 "
       pdb=" CG  LEU R  65 "
    ideal  model  delta    sigma   weight residual
    1.530  1.598 -0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" N   LEU R  37 "
       pdb=" CA  LEU R  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.13e+01
  bond pdb=" N   MET R 166 "
       pdb=" CA  MET R 166 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.12e+01
  bond pdb=" N   ASN R 297 "
       pdb=" CA  ASN R 297 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 9.20e-03 1.18e+04 1.08e+01
  ... (remaining 9026 not shown)

  Histogram of bond angle deviations from ideal:
       99.34 -   106.33: 194
      106.33 -   113.32: 4928
      113.32 -   120.31: 3530
      120.31 -   127.30: 3508
      127.30 -   134.29: 94
  Bond angle restraints: 12254
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     113.16  100.64   12.52 1.24e+00 6.50e-01 1.02e+02
  angle pdb=" N   PRO R  38 "
        pdb=" CA  PRO R  38 "
        pdb=" C   PRO R  38 "
      ideal   model   delta    sigma   weight residual
     110.70  119.62   -8.92 1.22e+00 6.72e-01 5.34e+01
  angle pdb=" CA  PRO R  38 "
        pdb=" C   PRO R  38 "
        pdb=" N   PRO R  39 "
      ideal   model   delta    sigma   weight residual
     117.93  123.08   -5.15 1.20e+00 6.94e-01 1.84e+01
  angle pdb=" N   GLN A 204 "
        pdb=" CA  GLN A 204 "
        pdb=" C   GLN A 204 "
      ideal   model   delta    sigma   weight residual
     108.24  101.02    7.22 1.81e+00 3.05e-01 1.59e+01
  angle pdb=" C   ILE R 247 "
        pdb=" CA  ILE R 247 "
        pdb=" CB  ILE R 247 "
      ideal   model   delta    sigma   weight residual
     111.97  106.87    5.10 1.28e+00 6.10e-01 1.59e+01
  ... (remaining 12249 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 4827
       16.06 -    32.12: 437
       32.12 -    48.18: 78
       48.18 -    64.24: 9
       64.24 -    80.31: 7
  Dihedral angle restraints: 5358
    sinusoidal: 2069
      harmonic: 3289
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 183 "
           pdb=" CB  CYS R 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.42   78.42     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.38   22.62     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  LYS S  76 "
           pdb=" C   LYS S  76 "
           pdb=" N   ASN S  77 "
           pdb=" CA  ASN S  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5355 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1142
       0.082 -    0.164: 216
       0.164 -    0.246: 42
       0.246 -    0.328: 7
       0.328 -    0.410: 1
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  PRO R  38 "
            pdb=" N   PRO R  38 "
            pdb=" C   PRO R  38 "
            pdb=" CB  PRO R  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.20e+00
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  LYS R 107 "
            pdb=" N   LYS R 107 "
            pdb=" C   LYS R 107 "
            pdb=" CB  LYS R 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  75 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.20e+01
        pdb=" C   GLN B  75 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLN B  75 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B  76 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 158 "   -0.039 2.00e-02 2.50e+03   1.98e-02 9.84e+00
        pdb=" CG  TRP R 158 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 158 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 158 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 158 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 158 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 158 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 158 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 158 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 158 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 306 "   -0.014 2.00e-02 2.50e+03   2.96e-02 8.74e+00
        pdb=" C   GLU R 306 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLU R 306 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG R 307 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2527
        2.81 -     3.33: 7942
        3.33 -     3.86: 14143
        3.86 -     4.38: 17397
        4.38 -     4.90: 29863
  Nonbonded interactions: 71872
  Sorted by model distance:
  nonbonded pdb=" O   MET B 325 "
            pdb=" OD1 ASN B 340 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG  SER S 161 "
            pdb=" O   LYS S 163 "
     model   vdw
     2.294 2.440
  nonbonded pdb=" NH1 ARG S  67 "
            pdb=" OD2 ASP S  90 "
     model   vdw
     2.295 2.520
  nonbonded pdb=" O   SER A 281 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.299 2.440
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.308 2.440
  ... (remaining 71867 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:             0.570
  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:             0.000
  Extract box with map and model:          2.990
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     27.490
  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:12.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
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      :  0.008   0.068   9031  Z= 0.489
  Angle     :  0.928  12.521  12254  Z= 0.654
  Chirality :  0.068   0.410   1408
  Planarity :  0.005   0.037   1529
  Dihedral  : 12.527  80.306   3233
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.45 (0.24), residues: 1116
  helix:  0.84 (0.26), residues: 391
  sheet: -1.55 (0.27), residues: 299
  loop : -2.18 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.039   0.003   TRP R 158 
   HIS   0.006   0.001   HIS R 293 
   PHE   0.017   0.002   PHE R 308 
   TYR   0.019   0.002   TYR S 175 
   ARG   0.008   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 1.0876
  time to fit residues: 207.6382
Evaluate side-chains
  101 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.009 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4703
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 99 optimal weight:   30.0000
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
B  91 HIS
** R 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 314 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9031  Z= 0.279
  Angle     :  0.581   7.757  12254  Z= 0.302
  Chirality :  0.043   0.168   1408
  Planarity :  0.004   0.036   1529
  Dihedral  :  4.727  49.220   1287
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 15.12 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.62 (0.24), residues: 1116
  helix:  1.54 (0.26), residues: 393
  sheet: -1.01 (0.30), residues: 274
  loop : -1.78 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.008   0.001   HIS R 293 
   PHE   0.014   0.001   PHE A 196 
   TYR   0.017   0.002   TYR S 227 
   ARG   0.004   0.000   ARG S 160 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 39
  outliers final: 15
  residues processed: 132
  average time/residue: 1.0313
  time to fit residues: 147.6406
Evaluate side-chains
  107 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 1.037 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 8
  residues processed: 7
  average time/residue: 0.5968
  time to fit residues: 6.1379
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    9.9990
   chunk 68 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0020
   chunk 100 optimal weight:   40.0000
   chunk 108 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 99 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    2.5194

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

Flipped N/Q/H residues before XYZ refinement:
** R 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   9031  Z= 0.424
  Angle     :  0.639   8.056  12254  Z= 0.333
  Chirality :  0.046   0.171   1408
  Planarity :  0.004   0.039   1529
  Dihedral  :  4.939  43.704   1287
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.78 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1116
  helix:  1.26 (0.26), residues: 396
  sheet: -1.02 (0.29), residues: 279
  loop : -1.59 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP R  90 
   HIS   0.009   0.001   HIS R 293 
   PHE   0.018   0.002   PHE R  83 
   TYR   0.018   0.002   TYR S 101 
   ARG   0.008   0.001   ARG S  87 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 101
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 20
  residues processed: 131
  average time/residue: 0.9945
  time to fit residues: 141.3860
Evaluate side-chains
  111 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 1.007 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 15
  residues processed: 5
  average time/residue: 0.6164
  time to fit residues: 4.9202
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 75 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 100 optimal weight:   50.0000
   chunk 106 optimal weight:   20.0000
   chunk 52 optimal weight:    0.7980
   chunk 95 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
R 181 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9031  Z= 0.167
  Angle     :  0.508   8.468  12254  Z= 0.264
  Chirality :  0.041   0.148   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.473  46.092   1287
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 19.49 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1116
  helix:  1.75 (0.27), residues: 396
  sheet: -0.78 (0.30), residues: 273
  loop : -1.37 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP B  82 
   HIS   0.006   0.001   HIS R 293 
   PHE   0.016   0.001   PHE R  45 
   TYR   0.014   0.001   TYR S 190 
   ARG   0.006   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
  outliers start: 37
  outliers final: 20
  residues processed: 129
  average time/residue: 1.0591
  time to fit residues: 147.5679
Evaluate side-chains
  118 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 16
  residues processed: 4
  average time/residue: 0.3943
  time to fit residues: 3.3358
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 73 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 125 ASN
S  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9031  Z= 0.269
  Angle     :  0.547  10.195  12254  Z= 0.282
  Chirality :  0.042   0.145   1408
  Planarity :  0.004   0.039   1529
  Dihedral  :  4.517  43.297   1287
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.66 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.20 (0.25), residues: 1116
  helix:  1.71 (0.27), residues: 395
  sheet: -0.83 (0.29), residues: 279
  loop : -1.33 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  82 
   HIS   0.006   0.001   HIS R 293 
   PHE   0.014   0.001   PHE R  45 
   TYR   0.020   0.001   TYR R  62 
   ARG   0.005   0.000   ARG S  87 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
  outliers start: 36
  outliers final: 24
  residues processed: 132
  average time/residue: 0.9030
  time to fit residues: 130.2020
Evaluate side-chains
  122 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.919 
Switching outliers to nearest non-outliers
  outliers start: 24
  outliers final: 20
  residues processed: 4
  average time/residue: 0.7685
  time to fit residues: 4.6481
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 331 ASN
B 125 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9031  Z= 0.232
  Angle     :  0.535   9.011  12254  Z= 0.275
  Chirality :  0.042   0.139   1408
  Planarity :  0.003   0.039   1529
  Dihedral  :  4.430  42.734   1287
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.51 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 (0.25), residues: 1116
  helix:  1.74 (0.27), residues: 397
  sheet: -0.80 (0.29), residues: 277
  loop : -1.27 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  82 
   HIS   0.006   0.001   HIS R 293 
   PHE   0.014   0.001   PHE R  45 
   TYR   0.013   0.001   TYR S 190 
   ARG   0.006   0.000   ARG S  87 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
  outliers start: 37
  outliers final: 27
  residues processed: 129
  average time/residue: 1.0083
  time to fit residues: 142.0270
Evaluate side-chains
  121 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.945 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 23
  residues processed: 4
  average time/residue: 0.5584
  time to fit residues: 3.8787
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 125 ASN
S 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9031  Z= 0.214
  Angle     :  0.525   9.187  12254  Z= 0.269
  Chirality :  0.041   0.139   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.320  40.688   1287
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.68 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.00 (0.25), residues: 1116
  helix:  1.79 (0.27), residues: 398
  sheet: -0.69 (0.30), residues: 276
  loop : -1.17 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  82 
   HIS   0.005   0.001   HIS R 293 
   PHE   0.023   0.001   PHE S 177 
   TYR   0.015   0.001   TYR S 190 
   ARG   0.007   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
  outliers start: 36
  outliers final: 29
  residues processed: 131
  average time/residue: 0.8995
  time to fit residues: 128.9069
Evaluate side-chains
  124 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 1.011 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 25
  residues processed: 4
  average time/residue: 0.6230
  time to fit residues: 4.1970
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0980
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 52 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0270
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9031  Z= 0.142
  Angle     :  0.498   9.315  12254  Z= 0.254
  Chirality :  0.040   0.140   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.061  37.064   1287
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.22 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.27 (0.26), residues: 1116
  helix:  1.98 (0.27), residues: 398
  sheet: -0.50 (0.30), residues: 275
  loop : -1.01 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP B  82 
   HIS   0.004   0.001   HIS R 293 
   PHE   0.025   0.001   PHE S 177 
   TYR   0.014   0.001   TYR S 190 
   ARG   0.006   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
  outliers start: 34
  outliers final: 26
  residues processed: 132
  average time/residue: 0.9254
  time to fit residues: 133.7262
Evaluate side-chains
  119 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 1.000 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 22
  residues processed: 4
  average time/residue: 0.1140
  time to fit residues: 2.1401
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0050
   chunk 89 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 255 ASN
B  75 GLN
B 125 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9031  Z= 0.220
  Angle     :  0.540   9.470  12254  Z= 0.273
  Chirality :  0.041   0.137   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.159  35.057   1287
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.75 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.22 (0.25), residues: 1116
  helix:  1.91 (0.27), residues: 398
  sheet: -0.50 (0.30), residues: 274
  loop : -1.03 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  82 
   HIS   0.005   0.001   HIS R 293 
   PHE   0.025   0.001   PHE S  68 
   TYR   0.026   0.001   TYR R  62 
   ARG   0.006   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 33
  outliers final: 25
  residues processed: 134
  average time/residue: 0.8149
  time to fit residues: 120.2201
Evaluate side-chains
  115 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 1.055 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 24
  residues processed: 1
  average time/residue: 0.0839
  time to fit residues: 1.6246
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9031  Z= 0.198
  Angle     :  0.553  14.289  12254  Z= 0.277
  Chirality :  0.041   0.139   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.138  34.341   1287
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.17 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.29 (0.26), residues: 1116
  helix:  1.89 (0.27), residues: 395
  sheet: -0.41 (0.30), residues: 285
  loop : -0.94 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  82 
   HIS   0.005   0.001   HIS R 293 
   PHE   0.029   0.001   PHE S 212 
   TYR   0.013   0.001   TYR S 190 
   ARG   0.005   0.000   ARG R 277 

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
  outliers start: 31
  outliers final: 28
  residues processed: 126
  average time/residue: 0.9010
  time to fit residues: 124.0631
Evaluate side-chains
  122 residues out of total 980 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.010 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 24
  residues processed: 4
  average time/residue: 0.3464
  time to fit residues: 3.0807
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0060
   chunk 24 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.222457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.134905 restraints weight = 8975.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 3.18
r_work: 0.3384 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6074
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9031  Z= 0.194
  Angle     :  0.540  13.290  12254  Z= 0.271
  Chirality :  0.041   0.142   1408
  Planarity :  0.003   0.037   1529
  Dihedral  :  4.114  31.876   1287
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.60 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.37 (0.26), residues: 1116
  helix:  1.95 (0.27), residues: 395
  sheet: -0.32 (0.30), residues: 281
  loop : -0.91 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  82 
   HIS   0.005   0.001   HIS R 293 
   PHE   0.031   0.001   PHE S 212 
   TYR   0.030   0.001   TYR R  62 
   ARG   0.005   0.000   ARG R 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3225.38 seconds
wall clock time: 58 minutes 18.51 seconds (3498.51 seconds total)