Starting phenix.real_space_refine
on Fri Nov 15 22:54:41 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ium_35726/11_2024/8ium_35726.cif"
  }
  resolution = 3.14
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    6307      2.51       5
     N    1716      2.21       5
     O    1860      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 9955
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1873
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 4, 'TRANS': 222}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2591
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "E"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1768
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 407
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2314
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 5, 'TRANS': 287}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'S2F': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.05, per 1000 atoms: 0.61
  Number of scatterers: 9955
  At special positions: 0
  Unit cell: (122.776, 88.992, 130.192, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     F       2      9.00
     O    1860      8.00
     N    1716      7.00
     C    6307      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 2.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      35.7% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.588A  pdb=" N   LYS A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 59
      removed outlier: 3.696A  pdb=" N   MET A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 4.219A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 3.511A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 285
      removed outlier: 3.728A  pdb=" N   TYR A 285 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 316
      removed outlier: 3.604A  pdb=" N   ALA A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 358
    Processing helix  chain 'B' and resid 9 through 30
      removed outlier: 3.838A  pdb=" N   CYS B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.740A  pdb=" N   ILE B  38 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 55
      removed outlier: 3.538A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 55'
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 4.003A  pdb=" N   THR E  90 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
      removed outlier: 3.758A  pdb=" N   ASN G  23 " --> pdb=" O   LYS G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 44
      removed outlier: 3.809A  pdb=" N   ALA G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.842A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.535A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 59
      removed outlier: 3.956A  pdb=" N   ARG R  57 " --> pdb=" O   LYS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 94
      removed outlier: 3.539A  pdb=" N   SER R  94 " --> pdb=" O   PHE R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 102
      removed outlier: 3.707A  pdb=" N   PHE R 101 " --> pdb=" O   GLU R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 106 through 139
      removed outlier: 4.386A  pdb=" N   SER R 118 " --> pdb=" O   CYS R 114 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   GLY R 119 " --> pdb=" O   MET R 115 " (cutoff:3.500A)
      Proline residue:  R 122  - end of helix
      removed outlier: 4.182A  pdb=" N   GLY R 126 " --> pdb=" O   PRO R 122 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 146
    Processing helix  chain 'R' and resid 148 through 168
    Processing helix  chain 'R' and resid 170 through 174
      removed outlier: 3.939A  pdb=" N   HIS R 174 " --> pdb=" O   ILE R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 233
      removed outlier: 4.162A  pdb=" N   ARG R 199 " --> pdb=" O   ASP R 195 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA R 212 " --> pdb=" O   LEU R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 243 through 276
      removed outlier: 3.831A  pdb=" N   MET R 247 " --> pdb=" O   HIS R 243 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   CYS R 259 " --> pdb=" O   MET R 255 " (cutoff:3.500A)
      Proline residue:  R 264  - end of helix
    Processing helix  chain 'R' and resid 277 through 279
      No H-bonds generated for 'chain 'R' and resid 277 through 279'
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 4.148A  pdb=" N   THR R 286 " --> pdb=" O   THR R 282 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 323
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 6.718A  pdb=" N   LEU A  40 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A  42 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 8.573A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ARG A  41 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.576A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU A  43 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57
      removed outlier: 4.655A  pdb=" N   PHE B 340 " --> pdb=" O   SER B 336 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   SER B 336 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 4.124A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   HIS B  96 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 7.103A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 4.306A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR B 164 " --> pdb=" O   ALA B 172 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA B 172 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   LEU B 173 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.555A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   THR B 226 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU B 215 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.224A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 6.664A  pdb=" N   GLY B 293 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   VAL B 281 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU B 291 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   PHE B 283 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   LEU B 289 " --> pdb=" O   PHE B 283 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   CYS B 299 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL B 312 " --> pdb=" O   CYS B 299 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   VAL B 301 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
      removed outlier: 3.807A  pdb=" N   ARG E  17 " --> pdb=" O   MET E  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU E  19 " --> pdb=" O   LEU E  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.075A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
      removed outlier: 3.668A  pdb=" N   THR E 141 " --> pdb=" O   ARG E 160 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG E 160 " --> pdb=" O   THR E 141 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 186 through 187
    Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.732A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA N  23 " --> pdb=" O   GLN N   5 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER N   7 " --> pdb=" O   SER N  21 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.085A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 178 through 179
      removed outlier: 3.636A  pdb=" N   PHE R 187 " --> pdb=" O   LYS R 178 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1332 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: 3.16

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1626
        1.31 -     1.44: 2811
        1.44 -     1.56: 5610
        1.56 -     1.68: 3
        1.68 -     1.81: 101
  Bond restraints: 10151
  Sorted by residual:
  bond pdb=" C10 S2F R 401 "
       pdb=" C11 S2F R 401 "
    ideal  model  delta    sigma   weight residual
    1.529  1.328  0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C13 S2F R 401 "
       pdb=" C14 S2F R 401 "
    ideal  model  delta    sigma   weight residual
    1.541  1.352  0.189 2.00e-02 2.50e+03 8.90e+01
  bond pdb=" C11 S2F R 401 "
       pdb=" C13 S2F R 401 "
    ideal  model  delta    sigma   weight residual
    1.534  1.687 -0.153 2.00e-02 2.50e+03 5.84e+01
  bond pdb=" CA  ILE R 298 "
       pdb=" C   ILE R 298 "
    ideal  model  delta    sigma   weight residual
    1.523  1.428  0.095 1.27e-02 6.20e+03 5.61e+01
  bond pdb=" CA  PHE R 117 "
       pdb=" C   PHE R 117 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.065 1.24e-02 6.50e+03 2.71e+01
  ... (remaining 10146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.63: 13680
        4.63 -     9.26: 41
        9.26 -    13.89: 5
       13.89 -    18.52: 0
       18.52 -    23.14: 1
  Bond angle restraints: 13727
  Sorted by residual:
  angle pdb=" C07 S2F R 401 "
        pdb=" C08 S2F R 401 "
        pdb=" C09 S2F R 401 "
      ideal   model   delta    sigma   weight residual
     128.15  105.01   23.14 3.00e+00 1.11e-01 5.95e+01
  angle pdb=" N   LEU R 208 "
        pdb=" CA  LEU R 208 "
        pdb=" C   LEU R 208 "
      ideal   model   delta    sigma   weight residual
     113.19  105.13    8.06 1.19e+00 7.06e-01 4.58e+01
  angle pdb=" N   ALA A  13 "
        pdb=" CA  ALA A  13 "
        pdb=" C   ALA A  13 "
      ideal   model   delta    sigma   weight residual
     112.89  104.97    7.92 1.24e+00 6.50e-01 4.07e+01
  angle pdb=" N   TRP R 295 "
        pdb=" CA  TRP R 295 "
        pdb=" C   TRP R 295 "
      ideal   model   delta    sigma   weight residual
     113.23  105.62    7.61 1.24e+00 6.50e-01 3.77e+01
  angle pdb=" N   ASP R 198 "
        pdb=" CA  ASP R 198 "
        pdb=" C   ASP R 198 "
      ideal   model   delta    sigma   weight residual
     111.07  104.52    6.55 1.07e+00 8.73e-01 3.74e+01
  ... (remaining 13722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 5833
       17.14 -    34.28: 184
       34.28 -    51.42: 32
       51.42 -    68.56: 6
       68.56 -    85.69: 1
  Dihedral angle restraints: 6056
    sinusoidal: 2389
      harmonic: 3667
  Sorted by residual:
  dihedral pdb=" C   CYS R 121 "
           pdb=" N   CYS R 121 "
           pdb=" CA  CYS R 121 "
           pdb=" CB  CYS R 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.32    9.72     0      2.50e+00 1.60e-01 1.51e+01
  dihedral pdb=" C   LEU R 203 "
           pdb=" N   LEU R 203 "
           pdb=" CA  LEU R 203 "
           pdb=" CB  LEU R 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.22    9.62     0      2.50e+00 1.60e-01 1.48e+01
  dihedral pdb=" C   ILE R 298 "
           pdb=" N   ILE R 298 "
           pdb=" CA  ILE R 298 "
           pdb=" CB  ILE R 298 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -112.91   -9.09     0      2.50e+00 1.60e-01 1.32e+01
  ... (remaining 6053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1459
       0.093 -    0.187: 74
       0.187 -    0.280: 6
       0.280 -    0.374: 7
       0.374 -    0.467: 4
  Chirality restraints: 1550
  Sorted by residual:
  chirality pdb=" CA  LEU R 203 "
            pdb=" N   LEU R 203 "
            pdb=" C   LEU R 203 "
            pdb=" CB  LEU R 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  CYS R 121 "
            pdb=" N   CYS R 121 "
            pdb=" C   CYS R 121 "
            pdb=" CB  CYS R 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  LEU R 120 "
            pdb=" N   LEU R 120 "
            pdb=" C   LEU R 120 "
            pdb=" CB  LEU R 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.81e+00
  ... (remaining 1547 not shown)

  Planarity restraints: 1739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 294 "    0.040 2.00e-02 2.50e+03   8.07e-02 6.52e+01
        pdb=" C   THR R 294 "   -0.140 2.00e-02 2.50e+03
        pdb=" O   THR R 294 "    0.054 2.00e-02 2.50e+03
        pdb=" N   TRP R 295 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 121 "    0.076 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO R 122 "   -0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO R 122 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO R 122 "    0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  36 "   -0.026 2.00e-02 2.50e+03   1.82e-02 6.62e+00
        pdb=" CG  TYR A  36 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  36 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1736 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2273
        2.79 -     3.32: 9206
        3.32 -     3.84: 16078
        3.84 -     4.37: 18468
        4.37 -     4.90: 32979
  Nonbonded interactions: 79004
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  70 "
            pdb=" O   PRO B 112 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" N   ILE R 298 "
            pdb=" N   LEU R 299 "
     model   vdw
     2.278 2.560
  nonbonded pdb=" OG  SER B  79 "
            pdb=" OD1 ASP B  81 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG  SER B 286 "
            pdb=" OD2 ASP G  47 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   GLY R  80 "
            pdb=" ND2 ASN R  84 "
     model   vdw
     2.305 3.120
  ... (remaining 78999 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.090
  Find NCS groups from input model:        0.130
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.201  10151  Z= 0.344
  Angle     :  0.675  23.145  13727  Z= 0.396
  Chirality :  0.051   0.467   1550
  Planarity :  0.004   0.112   1739
  Dihedral  :  8.235  85.694   3683
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.16 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.70 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.08 %
  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: -0.94 (0.22), residues: 1248
  helix:  0.95 (0.25), residues: 406
  sheet: -0.74 (0.29), residues: 293
  loop : -1.77 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 295 
 HIS   0.007   0.001   HIS B  59 
 PHE   0.020   0.001   PHE R 205 
 TYR   0.044   0.001   TYR A  36 
 ARG   0.002   0.000   ARG N 118 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 202
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8070 (mtpp)
REVERT: A  226 ASP cc_start: 0.7674 (t0) cc_final: 0.7435 (t0)
REVERT: A  343 ASP cc_start: 0.7822 (m-30) cc_final: 0.7590 (m-30)
REVERT: A  351 MET cc_start: 0.7475 (ttm) cc_final: 0.7239 (ttp)
REVERT: B  267 MET cc_start: 0.7937 (tpp) cc_final: 0.7702 (tpp)
REVERT: N   34 MET cc_start: 0.8066 (mmt) cc_final: 0.7823 (mmm)
REVERT: R  154 MET cc_start: 0.6408 (mtm) cc_final: 0.6084 (ptt)
  outliers start: 3
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2569
  time to fit residues: 70.6923
Evaluate side-chains
  117 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
A 238 ASN
A 327 HIS
B  18 GLN
B  93 ASN
B 225 GLN
B 271 HIS
E  34 HIS
E  81 GLN
E 142 GLN
E 167 HIS
G  17 GLN
N   5 GLN
N 120 GLN
R  56 GLN
R 244 HIS
** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 296 ASN
R 321 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  10151  Z= 0.353
  Angle     :  0.675   9.631  13727  Z= 0.351
  Chirality :  0.047   0.211   1550
  Planarity :  0.005   0.075   1739
  Dihedral  :  5.695  67.883   1410
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.66 %
    Favored  : 89.40 %
  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: -0.14 (0.23), residues: 1248
  helix:  1.53 (0.25), residues: 404
  sheet: -0.43 (0.28), residues: 328
  loop : -1.13 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 262 
 HIS   0.008   0.002   HIS R 243 
 PHE   0.025   0.003   PHE R 117 
 TYR   0.027   0.002   TYR E 190 
 ARG   0.007   0.001   ARG E 191 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8037 (mtpp)
REVERT: A  241 LYS cc_start: 0.7591 (tttt) cc_final: 0.7390 (ttpp)
REVERT: A  308 LYS cc_start: 0.7527 (tptt) cc_final: 0.7081 (ttpt)
REVERT: A  351 MET cc_start: 0.8020 (ttm) cc_final: 0.7592 (ttp)
REVERT: B  252 ASP cc_start: 0.5512 (t0) cc_final: 0.5115 (t0)
REVERT: B  280 SER cc_start: 0.8503 (t) cc_final: 0.8131 (p)
REVERT: E   16 SER cc_start: 0.8037 (m) cc_final: 0.7785 (t)
REVERT: E   17 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7808 (ttm-80)
REVERT: E  186 GLN cc_start: 0.7716 (tt0) cc_final: 0.7455 (tt0)
REVERT: N   34 MET cc_start: 0.8315 (mmt) cc_final: 0.8020 (mmm)
REVERT: R   74 VAL cc_start: 0.7491 (t) cc_final: 0.7257 (m)
  outliers start: 21
  outliers final: 12
  residues processed: 174
  average time/residue: 0.3107
  time to fit residues: 69.9075
Evaluate side-chains
  133 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain R residue  184 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0980
   chunk 76 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 111 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 90 optimal weight:   20.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
E 194 ASN
G  58 ASN
** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10151  Z= 0.217
  Angle     :  0.520   8.468  13727  Z= 0.273
  Chirality :  0.042   0.161   1550
  Planarity :  0.004   0.071   1739
  Dihedral  :  4.747  48.243   1410
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.06 %
    Favored  : 86.73 %
  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:  0.52 (0.24), residues: 1248
  helix:  2.14 (0.26), residues: 404
  sheet: -0.23 (0.28), residues: 334
  loop : -0.67 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 295 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.003   0.000   ARG A 247 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8056 (mtpp)
REVERT: A  206 ASP cc_start: 0.7106 (p0) cc_final: 0.6865 (p0)
REVERT: A  241 LYS cc_start: 0.7540 (tttt) cc_final: 0.7274 (ttmt)
REVERT: A  308 LYS cc_start: 0.7529 (tptt) cc_final: 0.7264 (ttpt)
REVERT: A  351 MET cc_start: 0.7961 (ttm) cc_final: 0.7489 (ttp)
REVERT: B  129 TYR cc_start: 0.8699 (m-80) cc_final: 0.8496 (m-80)
REVERT: B  219 ARG cc_start: 0.7763 (mpt-90) cc_final: 0.7480 (mpp80)
REVERT: B  248 THR cc_start: 0.8086 (p) cc_final: 0.7806 (p)
REVERT: E   16 SER cc_start: 0.8101 (m) cc_final: 0.7830 (t)
REVERT: N   34 MET cc_start: 0.8386 (mmt) cc_final: 0.8128 (mmm)
REVERT: N   59 SER cc_start: 0.6241 (m) cc_final: 0.5864 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2665
  time to fit residues: 57.3146
Evaluate side-chains
  143 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  259 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    0.2980
   chunk 84 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
G  58 ASN
R  81 HIS
** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 297 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10151  Z= 0.160
  Angle     :  0.468   6.503  13727  Z= 0.247
  Chirality :  0.040   0.163   1550
  Planarity :  0.004   0.063   1739
  Dihedral  :  4.480  39.695   1410
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.63 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1248
  helix:  2.53 (0.26), residues: 404
  sheet: -0.03 (0.28), residues: 331
  loop : -0.50 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 295 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.003   0.000   ARG A 247 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A  193 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8030 (mtpp)
REVERT: A  197 HIS cc_start: 0.6822 (m-70) cc_final: 0.6395 (m-70)
REVERT: A  308 LYS cc_start: 0.7662 (tptt) cc_final: 0.7274 (ttpt)
REVERT: A  351 MET cc_start: 0.7868 (ttm) cc_final: 0.7347 (ttp)
REVERT: B  129 TYR cc_start: 0.8572 (m-80) cc_final: 0.8349 (m-80)
REVERT: B  144 LEU cc_start: 0.7209 (pp) cc_final: 0.6938 (pt)
REVERT: B  248 THR cc_start: 0.8069 (p) cc_final: 0.7768 (p)
REVERT: E   16 SER cc_start: 0.8050 (m) cc_final: 0.7793 (t)
REVERT: E   17 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7700 (ttm-80)
REVERT: E  186 GLN cc_start: 0.7694 (tt0) cc_final: 0.7371 (tt0)
REVERT: G   20 MET cc_start: 0.6133 (mpp) cc_final: 0.5805 (mpp)
REVERT: N   59 SER cc_start: 0.6245 (m) cc_final: 0.5907 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 152
  average time/residue: 0.2696
  time to fit residues: 55.7009
Evaluate side-chains
  142 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain R residue   71 SER
Chi-restraints excluded: chain R residue  259 CYS
Chi-restraints excluded: chain R residue  297 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    0.0970
   chunk 68 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
A 204 GLN
E  81 GLN
** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10151  Z= 0.149
  Angle     :  0.463   6.869  13727  Z= 0.245
  Chirality :  0.040   0.166   1550
  Planarity :  0.003   0.056   1739
  Dihedral  :  4.631  52.993   1410
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.53 %
    Favored  : 84.98 %
  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:  1.15 (0.25), residues: 1248
  helix:  2.76 (0.26), residues: 402
  sheet:  0.08 (0.28), residues: 332
  loop : -0.34 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 295 
 HIS   0.009   0.001   HIS A 197 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.014   0.001   TYR E 190 
 ARG   0.002   0.000   ARG A 247 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  193 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8282 (mtmm)
REVERT: A  197 HIS cc_start: 0.6764 (m-70) cc_final: 0.6356 (m-70)
REVERT: A  237 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7566 (mp)
REVERT: A  308 LYS cc_start: 0.7665 (tptt) cc_final: 0.7250 (ttpt)
REVERT: B   60 LEU cc_start: 0.7698 (mt) cc_final: 0.7421 (mp)
REVERT: B  129 TYR cc_start: 0.8527 (m-80) cc_final: 0.8283 (m-80)
REVERT: B  183 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (p)
REVERT: B  219 ARG cc_start: 0.7686 (mpt-90) cc_final: 0.7332 (mpt-90)
REVERT: B  223 CYS cc_start: 0.8234 (p) cc_final: 0.7838 (p)
REVERT: B  225 GLN cc_start: 0.8548 (mt0) cc_final: 0.7995 (mt0)
REVERT: B  248 THR cc_start: 0.8062 (p) cc_final: 0.7751 (p)
REVERT: B  308 ASP cc_start: 0.7529 (m-30) cc_final: 0.6864 (p0)
REVERT: E   16 SER cc_start: 0.8025 (m) cc_final: 0.7802 (t)
REVERT: E  186 GLN cc_start: 0.7655 (tt0) cc_final: 0.7357 (tt0)
REVERT: N   59 SER cc_start: 0.6227 (m) cc_final: 0.5934 (p)
REVERT: R  129 MET cc_start: 0.7675 (mtp) cc_final: 0.7283 (mtp)
  outliers start: 27
  outliers final: 18
  residues processed: 146
  average time/residue: 0.2774
  time to fit residues: 53.9687
Evaluate side-chains
  143 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain N residue  125 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 119 optimal weight:   10.0000
   chunk 99 optimal weight:    0.0870
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
E  81 GLN
R 250 GLN
R 297 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.5925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10151  Z= 0.296
  Angle     :  0.562   8.442  13727  Z= 0.296
  Chirality :  0.043   0.180   1550
  Planarity :  0.004   0.056   1739
  Dihedral  :  5.061  78.220   1410
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.00 %
    Favored  : 84.33 %
  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:  0.98 (0.24), residues: 1248
  helix:  2.48 (0.26), residues: 403
  sheet:  0.08 (0.29), residues: 328
  loop : -0.40 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP R 295 
 HIS   0.014   0.002   HIS A 197 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.026   0.002   TYR E 190 
 ARG   0.002   0.000   ARG B  53 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 1.138 
Fit side-chains
REVERT: A  193 LYS cc_start: 0.8468 (ttmm) cc_final: 0.7905 (mtpp)
REVERT: A  197 HIS cc_start: 0.6841 (m-70) cc_final: 0.6437 (m-70)
REVERT: A  241 LYS cc_start: 0.7640 (tttt) cc_final: 0.7344 (ttmt)
REVERT: A  308 LYS cc_start: 0.7784 (tptt) cc_final: 0.7287 (ttpt)
REVERT: B  202 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.6841 (mmt-90)
REVERT: B  219 ARG cc_start: 0.7647 (mpt-90) cc_final: 0.7155 (mpt-90)
REVERT: B  223 CYS cc_start: 0.8193 (p) cc_final: 0.7789 (p)
REVERT: B  225 GLN cc_start: 0.8547 (mt0) cc_final: 0.8039 (mt0)
REVERT: B  248 THR cc_start: 0.8185 (p) cc_final: 0.7845 (p)
REVERT: E   16 SER cc_start: 0.8397 (m) cc_final: 0.8153 (t)
REVERT: E   17 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7890 (ttm-80)
REVERT: E  158 SER cc_start: 0.8780 (t) cc_final: 0.8346 (p)
REVERT: E  186 GLN cc_start: 0.7740 (tt0) cc_final: 0.7404 (tt0)
REVERT: E  234 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7259 (mt-10)
REVERT: N   59 SER cc_start: 0.6303 (m) cc_final: 0.5961 (p)
  outliers start: 29
  outliers final: 24
  residues processed: 149
  average time/residue: 0.2766
  time to fit residues: 55.4219
Evaluate side-chains
  148 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   70 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   71 SER
Chi-restraints excluded: chain R residue  297 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 119 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
R 297 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10151  Z= 0.160
  Angle     :  0.483   8.340  13727  Z= 0.255
  Chirality :  0.040   0.169   1550
  Planarity :  0.004   0.051   1739
  Dihedral  :  4.784  83.204   1410
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.18 %
    Favored  : 84.42 %
  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:  1.18 (0.24), residues: 1248
  helix:  2.75 (0.26), residues: 403
  sheet:  0.14 (0.29), residues: 326
  loop : -0.33 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 211 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.007   0.000   ARG A 247 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 1.302 
Fit side-chains
REVERT: A  193 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7912 (mtpp)
REVERT: A  197 HIS cc_start: 0.6817 (m-70) cc_final: 0.6463 (m-70)
REVERT: A  307 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7249 (ttp80)
REVERT: A  308 LYS cc_start: 0.7681 (tptt) cc_final: 0.7261 (ttpt)
REVERT: B  183 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8239 (p)
REVERT: B  219 ARG cc_start: 0.7637 (mpt-90) cc_final: 0.7252 (mpt-90)
REVERT: B  223 CYS cc_start: 0.8152 (p) cc_final: 0.7791 (p)
REVERT: B  225 GLN cc_start: 0.8521 (mt0) cc_final: 0.8130 (mt0)
REVERT: B  248 THR cc_start: 0.8058 (p) cc_final: 0.7711 (p)
REVERT: B  308 ASP cc_start: 0.7353 (m-30) cc_final: 0.6834 (p0)
REVERT: E   30 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8077 (p)
REVERT: E  158 SER cc_start: 0.8641 (t) cc_final: 0.8219 (p)
REVERT: E  186 GLN cc_start: 0.7770 (tt0) cc_final: 0.7463 (tt0)
REVERT: N   59 SER cc_start: 0.6270 (m) cc_final: 0.5984 (p)
REVERT: R  314 ASN cc_start: 0.7111 (t0) cc_final: 0.6909 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 149
  average time/residue: 0.2578
  time to fit residues: 52.2847
Evaluate side-chains
  141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   71 SER
Chi-restraints excluded: chain R residue  297 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 71 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 93 optimal weight:    0.2980
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.5946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10151  Z= 0.176
  Angle     :  0.487   9.574  13727  Z= 0.256
  Chirality :  0.041   0.170   1550
  Planarity :  0.004   0.050   1739
  Dihedral  :  4.845  95.627   1410
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.73 %
    Favored  : 83.96 %
  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:  1.24 (0.24), residues: 1248
  helix:  2.83 (0.25), residues: 401
  sheet:  0.12 (0.29), residues: 326
  loop : -0.27 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 295 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.017   0.001   TYR E 190 
 ARG   0.006   0.000   ARG A 247 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A  197 HIS cc_start: 0.6792 (m-70) cc_final: 0.6442 (m-70)
REVERT: A  307 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7296 (ttp80)
REVERT: A  308 LYS cc_start: 0.7768 (tptt) cc_final: 0.7343 (ttpt)
REVERT: B  183 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8254 (p)
REVERT: B  202 ARG cc_start: 0.7458 (mmt-90) cc_final: 0.7049 (mmt180)
REVERT: B  219 ARG cc_start: 0.7660 (mpt-90) cc_final: 0.7432 (mpp80)
REVERT: B  223 CYS cc_start: 0.8144 (p) cc_final: 0.7797 (p)
REVERT: B  225 GLN cc_start: 0.8519 (mt0) cc_final: 0.8158 (mt0)
REVERT: B  248 THR cc_start: 0.8050 (p) cc_final: 0.7708 (p)
REVERT: B  308 ASP cc_start: 0.7403 (m-30) cc_final: 0.6828 (p0)
REVERT: E   30 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8032 (p)
REVERT: E  158 SER cc_start: 0.8681 (t) cc_final: 0.8232 (p)
REVERT: E  186 GLN cc_start: 0.7808 (tt0) cc_final: 0.7319 (tt0)
REVERT: N   59 SER cc_start: 0.6278 (m) cc_final: 0.6011 (p)
REVERT: R  129 MET cc_start: 0.7645 (mtp) cc_final: 0.7326 (mtp)
  outliers start: 25
  outliers final: 19
  residues processed: 140
  average time/residue: 0.2577
  time to fit residues: 49.1223
Evaluate side-chains
  139 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   71 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 110 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.6146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10151  Z= 0.224
  Angle     :  0.520   9.154  13727  Z= 0.272
  Chirality :  0.041   0.174   1550
  Planarity :  0.004   0.052   1739
  Dihedral  :  4.933  90.157   1410
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.01 %
    Favored  : 83.87 %
  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:  1.19 (0.24), residues: 1248
  helix:  2.80 (0.25), residues: 397
  sheet:  0.17 (0.29), residues: 324
  loop : -0.33 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 174 
 HIS   0.010   0.001   HIS A 197 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.021   0.001   TYR E 190 
 ARG   0.006   0.000   ARG E  17 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 HIS cc_start: 0.6815 (m-70) cc_final: 0.6529 (m-70)
REVERT: A  307 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7341 (ttp80)
REVERT: A  308 LYS cc_start: 0.7689 (tptt) cc_final: 0.7229 (ttpt)
REVERT: B  183 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (p)
REVERT: B  202 ARG cc_start: 0.7449 (mmt-90) cc_final: 0.7060 (mmt180)
REVERT: B  219 ARG cc_start: 0.7706 (mpt-90) cc_final: 0.7465 (mpp80)
REVERT: B  223 CYS cc_start: 0.8112 (p) cc_final: 0.7827 (p)
REVERT: B  225 GLN cc_start: 0.8544 (mt0) cc_final: 0.8172 (mt0)
REVERT: B  248 THR cc_start: 0.8042 (p) cc_final: 0.7743 (p)
REVERT: B  308 ASP cc_start: 0.7536 (m-30) cc_final: 0.6758 (p0)
REVERT: E   30 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8049 (p)
REVERT: E  158 SER cc_start: 0.8732 (t) cc_final: 0.8279 (p)
REVERT: E  186 GLN cc_start: 0.7807 (tt0) cc_final: 0.7510 (tt0)
REVERT: N   59 SER cc_start: 0.6486 (m) cc_final: 0.6234 (p)
REVERT: R  129 MET cc_start: 0.7711 (mtp) cc_final: 0.7361 (mtp)
  outliers start: 23
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2564
  time to fit residues: 49.9797
Evaluate side-chains
  143 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   71 SER
Chi-restraints excluded: chain R residue  184 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0040
   chunk 55 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.7394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.6101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10151  Z= 0.157
  Angle     :  0.478   9.729  13727  Z= 0.253
  Chirality :  0.040   0.169   1550
  Planarity :  0.004   0.051   1739
  Dihedral  :  4.792  88.199   1410
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.47 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.24), residues: 1248
  helix:  2.89 (0.25), residues: 397
  sheet:  0.24 (0.29), residues: 324
  loop : -0.27 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.005   0.001   HIS A 197 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.006   0.000   ARG A 307 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 HIS cc_start: 0.6762 (m-70) cc_final: 0.6513 (m-70)
REVERT: A  198 MET cc_start: 0.8712 (ttp) cc_final: 0.8336 (ttp)
REVERT: A  308 LYS cc_start: 0.7715 (tptt) cc_final: 0.7263 (ttpt)
REVERT: B  202 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7040 (mmt180)
REVERT: B  219 ARG cc_start: 0.7733 (mpt-90) cc_final: 0.7471 (mpp80)
REVERT: B  223 CYS cc_start: 0.8082 (p) cc_final: 0.7868 (p)
REVERT: B  225 GLN cc_start: 0.8522 (mt0) cc_final: 0.8226 (mt0)
REVERT: B  248 THR cc_start: 0.7951 (p) cc_final: 0.7619 (p)
REVERT: B  308 ASP cc_start: 0.7454 (m-30) cc_final: 0.6718 (p0)
REVERT: E   30 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8064 (p)
REVERT: E  158 SER cc_start: 0.8666 (t) cc_final: 0.8217 (p)
REVERT: E  186 GLN cc_start: 0.7786 (tt0) cc_final: 0.7316 (tt0)
REVERT: R   53 LYS cc_start: 0.7335 (mttt) cc_final: 0.6846 (mmtt)
REVERT: R  129 MET cc_start: 0.7644 (mtp) cc_final: 0.7316 (mtp)
  outliers start: 22
  outliers final: 20
  residues processed: 141
  average time/residue: 0.2517
  time to fit residues: 48.6058
Evaluate side-chains
  142 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  330 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain E residue   22 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   66 ARG
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   71 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 90 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0770
   chunk 86 optimal weight:   10.0000
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.177737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133396 restraints weight = 9945.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.87
r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.5982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10151  Z= 0.125
  Angle     :  0.452   9.605  13727  Z= 0.239
  Chirality :  0.039   0.165   1550
  Planarity :  0.003   0.049   1739
  Dihedral  :  4.643  84.260   1410
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.65 %
    Favored  : 83.13 %
  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:  1.45 (0.25), residues: 1248
  helix:  2.94 (0.25), residues: 406
  sheet:  0.39 (0.30), residues: 312
  loop : -0.23 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 197 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.007   0.000   ARG A 307 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2353.24 seconds
wall clock time: 43 minutes 50.42 seconds (2630.42 seconds total)