Starting phenix.real_space_refine
on Thu Mar 14 16:16:15 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq3_32698/03_2024/7wq3_32698_updated.pdb"
  }
  resolution = 2.7
  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: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5915      2.51       5
     N    1548      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9209
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2303
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 13, 'TRANS': 275}
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 117
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "R"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.22, per 1000 atoms: 0.57
  Number of scatterers: 9209
  At special positions: 0
  Unit cell: (110.16, 125.46, 123.42, 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      61     16.00
     O    1685      8.00
     N    1548      7.00
     C    5915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 187 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      35.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 60
      removed outlier: 4.618A  pdb=" N   VAL R  38 " --> pdb=" O   PHE R  34 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 97
      removed outlier: 3.754A  pdb=" N   ILE R  89 " --> pdb=" O   LEU R  85 " (cutoff:3.500A)
      Proline residue:  R  90  - end of helix
      removed outlier: 4.257A  pdb=" N   THR R  94 " --> pdb=" O   PRO R  90 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL R  95 " --> pdb=" O   PHE R  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR R  96 " --> pdb=" O   GLN R  92 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 135
      removed outlier: 4.149A  pdb=" N   HIS R 112 " --> pdb=" O   CYS R 108 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 146
      No H-bonds generated for 'chain 'R' and resid 143 through 146'
    Processing helix  chain 'R' and resid 149 through 166
    Processing helix  chain 'R' and resid 168 through 173
    Processing helix  chain 'R' and resid 194 through 208
      removed outlier: 3.715A  pdb=" N   ALA R 199 " --> pdb=" O   ARG R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 230
    Processing helix  chain 'R' and resid 236 through 259
    Processing helix  chain 'R' and resid 261 through 271
    Processing helix  chain 'R' and resid 279 through 302
      removed outlier: 3.780A  pdb=" N   SER R 296 " --> pdb=" O   ALA R 292 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
    Processing helix  chain 'R' and resid 308 through 317
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 4.215A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 4.166A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 277
      removed outlier: 4.360A  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 310
      removed outlier: 3.884A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.627A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 3.942A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 3.605A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (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 helix  chain 'S' and resid 53 through 55
      No H-bonds generated for 'chain 'S' and resid 53 through 55'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing helix  chain 'S' and resid 221 through 223
      No H-bonds generated for 'chain 'S' and resid 221 through 223'
    Processing helix  chain 'L' and resid 4 through 11
    Processing sheet with id=  A, first strand: chain 'R' and resid 175 through 178
    Processing sheet with id=  B, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.591A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.033A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.010A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.864A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.177A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.902A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.620A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.973A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (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: 5.864A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.284A  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: 7.287A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 155 through 160

    418 hydrogen bonds defined for protein.
    1200 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: 2.62

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2915
        1.34 -     1.46: 2281
        1.46 -     1.58: 4113
        1.58 -     1.70: 25
        1.70 -     1.81: 91
  Bond restraints: 9425
  Sorted by residual:
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.652 -0.320 2.00e-02 2.50e+03 2.56e+02
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 405 "
       pdb=" C6  CLR R 405 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 404 "
       pdb=" C6  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.332  1.650 -0.318 2.00e-02 2.50e+03 2.53e+02
  ... (remaining 9420 not shown)

  Histogram of bond angle deviations from ideal:
      100.60 -   107.28: 313
      107.28 -   113.96: 5396
      113.96 -   120.63: 3710
      120.63 -   127.31: 3275
      127.31 -   133.99: 103
  Bond angle restraints: 12797
  Sorted by residual:
  angle pdb=" C5  CLR R 405 "
        pdb=" C6  CLR R 405 "
        pdb=" C7  CLR R 405 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 403 "
        pdb=" C6  CLR R 403 "
        pdb=" C7  CLR R 403 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 402 "
        pdb=" C6  CLR R 402 "
        pdb=" C7  CLR R 402 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C5  CLR R 404 "
        pdb=" C6  CLR R 404 "
        pdb=" C7  CLR R 404 "
      ideal   model   delta    sigma   weight residual
     125.11  111.82   13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C4  CLR R 401 "
        pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     120.33  107.93   12.40 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 12792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 5564
       15.56 -    31.12: 165
       31.12 -    46.68: 53
       46.68 -    62.24: 23
       62.24 -    77.79: 3
  Dihedral angle restraints: 5808
    sinusoidal: 2443
      harmonic: 3365
  Sorted by residual:
  dihedral pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
           pdb=" CB  ARG S 191 "
           pdb=" CG  ARG S 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.85   59.85     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   PHE B 234 "
           pdb=" CA  PHE B 234 "
           pdb=" CB  PHE B 234 "
           pdb=" CG  PHE B 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.95  -57.05     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   PHE R 114 "
           pdb=" CA  PHE R 114 "
           pdb=" CB  PHE R 114 "
           pdb=" CG  PHE R 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.13   53.13     3      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 5805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1408
       0.112 -    0.223: 29
       0.223 -    0.335: 11
       0.335 -    0.446: 4
       0.446 -    0.558: 5
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" C13 CLR R 405 "
            pdb=" C12 CLR R 405 "
            pdb=" C14 CLR R 405 "
            pdb=" C17 CLR R 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.37   -0.56 2.00e-01 2.50e+01 7.78e+00
  chirality pdb=" C13 CLR R 404 "
            pdb=" C12 CLR R 404 "
            pdb=" C14 CLR R 404 "
            pdb=" C17 CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 299 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO R 300 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO S  41 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO B 236 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 438
        2.73 -     3.27: 9064
        3.27 -     3.82: 14967
        3.82 -     4.36: 17842
        4.36 -     4.90: 31261
  Nonbonded interactions: 73572
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 248 "
            pdb=" OD1 ASP A 251 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.243 2.440
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.248 2.440
  nonbonded pdb=" O   PHE S  29 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.263 2.520
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.269 2.440
  ... (remaining 73567 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.930
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.950
  Find NCS groups from input model:        0.280
  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:10.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4588
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      :  0.011   0.320   9425  Z= 0.680
  Angle     :  0.724  13.301  12797  Z= 0.335
  Chirality :  0.061   0.558   1457
  Planarity :  0.003   0.032   1586
  Dihedral  :  9.420  77.794   3633
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  2.43 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.34 (0.23), residues: 1144
  helix:  0.07 (0.25), residues: 408
  sheet: -1.00 (0.27), residues: 292
  loop : -1.59 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.006   0.001   TYR S 102 
 ARG   0.002   0.000   ARG B  68 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 ASN cc_start: 0.6883 (m110) cc_final: 0.6622 (m110)
REVERT: R  244 LYS cc_start: 0.6246 (mttt) cc_final: 0.5999 (mtmm)
REVERT: A  248 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6377 (tmmm)
REVERT: A  266 LEU cc_start: 0.5029 (tp) cc_final: 0.4807 (tm)
REVERT: A  276 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0)
REVERT: A  305 CYS cc_start: 0.6720 (m) cc_final: 0.6438 (m)
REVERT: A  314 LYS cc_start: 0.6025 (mttt) cc_final: 0.5625 (tppt)
REVERT: A  342 VAL cc_start: 0.6855 (t) cc_final: 0.6526 (m)
REVERT: G   20 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6256 (pttm)
REVERT: G   60 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6097 (Cg_exo)
REVERT: S   53 SER cc_start: 0.6534 (t) cc_final: 0.6274 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 231
  average time/residue: 0.9548
  time to fit residues: 238.0157
Evaluate side-chains
  136 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
A 204 GLN
B  91 HIS
B 176 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
S  39 GLN
S 142 GLN
S 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9425  Z= 0.241
  Angle     :  0.650   9.758  12797  Z= 0.325
  Chirality :  0.043   0.169   1457
  Planarity :  0.004   0.047   1586
  Dihedral  :  6.747  58.963   1574
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.65 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.10 (0.25), residues: 1144
  helix:  1.30 (0.28), residues: 395
  sheet: -0.37 (0.30), residues: 279
  loop : -1.00 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  99 
 HIS   0.010   0.002   HIS B 142 
 PHE   0.036   0.002   PHE R  91 
 TYR   0.014   0.002   TYR G  40 
 ARG   0.005   0.001   ARG S 191 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 SER cc_start: 0.7088 (m) cc_final: 0.6111 (p)
REVERT: A   10 LYS cc_start: 0.6754 (mttt) cc_final: 0.6512 (mttp)
REVERT: A   53 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4884 (tpp)
REVERT: A  198 MET cc_start: 0.7761 (mtp) cc_final: 0.7298 (mtm)
REVERT: A  248 LYS cc_start: 0.7103 (ttmm) cc_final: 0.6774 (tmmm)
REVERT: A  276 GLU cc_start: 0.7605 (mp0) cc_final: 0.7136 (mp0)
REVERT: A  305 CYS cc_start: 0.7073 (m) cc_final: 0.6695 (m)
REVERT: A  333 GLN cc_start: 0.6355 (mm-40) cc_final: 0.6135 (tp-100)
REVERT: B   61 MET cc_start: 0.7392 (tmt) cc_final: 0.7038 (tmt)
REVERT: B  134 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6663 (mtp-110)
REVERT: S   46 GLU cc_start: 0.6844 (pt0) cc_final: 0.6568 (pt0)
REVERT: S   58 ILE cc_start: 0.6012 (mt) cc_final: 0.5761 (mt)
REVERT: S   83 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7869 (ptp)
  outliers start: 31
  outliers final: 10
  residues processed: 196
  average time/residue: 1.0133
  time to fit residues: 213.7182
Evaluate side-chains
  144 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  164 SER
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
R 228 HIS
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  88 ASN
B 125 ASN
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S 142 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.9324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9425  Z= 0.323
  Angle     :  0.714   9.251  12797  Z= 0.371
  Chirality :  0.047   0.184   1457
  Planarity :  0.005   0.053   1586
  Dihedral  :  6.454  58.286   1574
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 14.47 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.08 (0.25), residues: 1144
  helix:  1.38 (0.27), residues: 389
  sheet: -0.16 (0.29), residues: 300
  loop : -0.90 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  63 
 HIS   0.011   0.002   HIS B  54 
 PHE   0.032   0.002   PHE R 115 
 TYR   0.020   0.002   TYR B 105 
 ARG   0.007   0.001   ARG S 180 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 187
  time to evaluate  : 0.897 
Fit side-chains
REVERT: R   78 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7269 (m)
REVERT: R  115 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7031 (p90)
REVERT: R  118 SER cc_start: 0.8061 (m) cc_final: 0.7592 (p)
REVERT: R  119 MET cc_start: 0.7030 (ptt) cc_final: 0.6793 (OUTLIER)
REVERT: R  234 MET cc_start: 0.7302 (mmm) cc_final: 0.6941 (mmp)
REVERT: R  252 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6428 (m)
REVERT: A   17 LYS cc_start: 0.6257 (mttt) cc_final: 0.5829 (mtmt)
REVERT: A   22 ASN cc_start: 0.7123 (m-40) cc_final: 0.6883 (m110)
REVERT: A   25 GLU cc_start: 0.6113 (tt0) cc_final: 0.5499 (tm-30)
REVERT: A   28 GLU cc_start: 0.7122 (tt0) cc_final: 0.6567 (mt-10)
REVERT: A  209 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6988 (mmtm)
REVERT: B   16 ASN cc_start: 0.5803 (m-40) cc_final: 0.5500 (m110)
REVERT: B   42 ARG cc_start: 0.5973 (tpt170) cc_final: 0.5719 (tmt170)
REVERT: B   98 SER cc_start: 0.8534 (m) cc_final: 0.8286 (t)
REVERT: B  130 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6024 (mp0)
REVERT: B  134 ARG cc_start: 0.7373 (mtp180) cc_final: 0.6867 (ptp90)
REVERT: B  137 ARG cc_start: 0.7022 (mmp80) cc_final: 0.6490 (tpt170)
REVERT: B  215 GLU cc_start: 0.7325 (mp0) cc_final: 0.7080 (mt-10)
REVERT: B  226 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7709 (pm20)
REVERT: B  268 ASN cc_start: 0.6984 (t0) cc_final: 0.6621 (m-40)
REVERT: B  277 SER cc_start: 0.8569 (t) cc_final: 0.7818 (p)
REVERT: B  304 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7436 (ttp80)
REVERT: G   46 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7435 (pmtt)
REVERT: G   47 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6831 (mt-10)
REVERT: G   58 GLU cc_start: 0.6728 (mp0) cc_final: 0.6066 (tm-30)
REVERT: S   46 GLU cc_start: 0.7859 (pt0) cc_final: 0.7172 (pt0)
REVERT: S   65 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6602 (tttp)
REVERT: S   71 SER cc_start: 0.7501 (OUTLIER) cc_final: 0.7194 (p)
REVERT: S  183 GLN cc_start: 0.6388 (mm110) cc_final: 0.6131 (mp-120)
REVERT: S  191 ARG cc_start: 0.2126 (OUTLIER) cc_final: 0.1511 (tpp80)
  outliers start: 47
  outliers final: 12
  residues processed: 219
  average time/residue: 1.0978
  time to fit residues: 257.7172
Evaluate side-chains
  155 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  191 ARG
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
R 225 ASN
A  52 GLN
A 204 GLN
A 256 ASN
B 156 GLN
B 176 GLN
B 230 ASN
B 340 ASN
S 171 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          1.0324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9425  Z= 0.301
  Angle     :  0.631   8.319  12797  Z= 0.328
  Chirality :  0.045   0.172   1457
  Planarity :  0.004   0.059   1586
  Dihedral  :  6.189  53.240   1574
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.12 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: 1144
  helix:  1.55 (0.27), residues: 388
  sheet: -0.05 (0.30), residues: 281
  loop : -0.90 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.008   0.001   HIS B  54 
 PHE   0.030   0.002   PHE R 115 
 TYR   0.018   0.002   TYR B 105 
 ARG   0.005   0.001   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 1.168 
Fit side-chains
REVERT: R   78 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7073 (m)
REVERT: R  119 MET cc_start: 0.7155 (ptt) cc_final: 0.6930 (ttp)
REVERT: R  234 MET cc_start: 0.7296 (mmm) cc_final: 0.7039 (mmp)
REVERT: R  252 VAL cc_start: 0.7210 (OUTLIER) cc_final: 0.6890 (m)
REVERT: A   17 LYS cc_start: 0.6370 (mttt) cc_final: 0.5997 (mtmt)
REVERT: A   22 ASN cc_start: 0.7116 (m-40) cc_final: 0.6728 (m110)
REVERT: A   25 GLU cc_start: 0.6091 (tt0) cc_final: 0.5497 (tm-30)
REVERT: A   26 ASP cc_start: 0.7025 (m-30) cc_final: 0.6631 (m-30)
REVERT: A   28 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6471 (mt-10)
REVERT: A  209 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7100 (mmtm)
REVERT: A  229 ASP cc_start: 0.6910 (m-30) cc_final: 0.6353 (p0)
REVERT: A  272 ASP cc_start: 0.6625 (m-30) cc_final: 0.6378 (m-30)
REVERT: A  273 LEU cc_start: 0.7386 (tp) cc_final: 0.6884 (tp)
REVERT: B   32 GLN cc_start: 0.8239 (mt0) cc_final: 0.7988 (mt0)
REVERT: B   42 ARG cc_start: 0.6240 (tpt170) cc_final: 0.5904 (tmt170)
REVERT: B  130 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6157 (mp0)
REVERT: B  134 ARG cc_start: 0.7345 (mtp180) cc_final: 0.6907 (ptp90)
REVERT: B  137 ARG cc_start: 0.7151 (mmp80) cc_final: 0.6676 (tpt170)
REVERT: B  138 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7966 (mt-10)
REVERT: B  172 GLU cc_start: 0.6928 (tp30) cc_final: 0.6543 (mt-10)
REVERT: B  226 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7688 (pm20)
REVERT: G   26 ASP cc_start: 0.7570 (t0) cc_final: 0.7180 (p0)
REVERT: G   58 GLU cc_start: 0.6856 (mp0) cc_final: 0.5907 (tm-30)
REVERT: S   46 GLU cc_start: 0.7939 (pt0) cc_final: 0.7276 (pt0)
REVERT: S   65 LYS cc_start: 0.7154 (ttmt) cc_final: 0.6646 (tttm)
REVERT: S   71 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.7111 (p)
REVERT: S   98 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7751 (ttp-170)
REVERT: S  140 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.6847 (mmm)
REVERT: S  160 ARG cc_start: 0.7324 (ptt180) cc_final: 0.6011 (mtm-85)
REVERT: S  186 GLN cc_start: 0.7441 (tt0) cc_final: 0.7179 (tt0)
  outliers start: 47
  outliers final: 20
  residues processed: 165
  average time/residue: 1.2512
  time to fit residues: 219.9771
Evaluate side-chains
  162 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  141 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 ASN
A  52 GLN
A 204 GLN
B 266 HIS
B 268 ASN
B 340 ASN
G  18 GLN
S  77 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          1.0684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9425  Z= 0.200
  Angle     :  0.543   8.015  12797  Z= 0.281
  Chirality :  0.042   0.147   1457
  Planarity :  0.004   0.055   1586
  Dihedral  :  5.673  56.865   1574
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 19.84 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1144
  helix:  1.87 (0.27), residues: 391
  sheet:  0.04 (0.29), residues: 284
  loop : -0.72 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.023   0.001   PHE R 115 
 TYR   0.009   0.001   TYR S 190 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 139
  time to evaluate  : 0.920 
Fit side-chains
REVERT: R  234 MET cc_start: 0.7352 (mmm) cc_final: 0.7106 (mmp)
REVERT: R  252 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6784 (m)
REVERT: A   17 LYS cc_start: 0.6217 (mttt) cc_final: 0.5842 (mtmt)
REVERT: A   22 ASN cc_start: 0.6882 (m-40) cc_final: 0.6600 (m110)
REVERT: A   25 GLU cc_start: 0.6169 (tt0) cc_final: 0.5564 (tm-30)
REVERT: A   28 GLU cc_start: 0.6975 (tt0) cc_final: 0.6465 (mt-10)
REVERT: A  209 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7076 (mmtm)
REVERT: A  251 ASP cc_start: 0.7587 (t0) cc_final: 0.7347 (t0)
REVERT: B   19 ARG cc_start: 0.6262 (ttp80) cc_final: 0.6059 (ttp80)
REVERT: B   32 GLN cc_start: 0.8190 (mt0) cc_final: 0.7983 (mt0)
REVERT: B   42 ARG cc_start: 0.6332 (tpt170) cc_final: 0.6001 (tmt170)
REVERT: B  130 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6075 (mp0)
REVERT: B  134 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6891 (ptp90)
REVERT: B  135 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (p)
REVERT: B  137 ARG cc_start: 0.6897 (mmp80) cc_final: 0.6481 (tpt170)
REVERT: B  172 GLU cc_start: 0.6913 (tp30) cc_final: 0.6535 (mt-10)
REVERT: B  226 GLU cc_start: 0.8245 (pt0) cc_final: 0.7680 (pm20)
REVERT: B  312 ASP cc_start: 0.7672 (m-30) cc_final: 0.7322 (m-30)
REVERT: G   58 GLU cc_start: 0.6729 (mp0) cc_final: 0.5872 (tm-30)
REVERT: S   46 GLU cc_start: 0.7973 (pt0) cc_final: 0.7330 (pt0)
REVERT: S   65 LYS cc_start: 0.7196 (ttmt) cc_final: 0.6849 (ttpt)
REVERT: S   71 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.7049 (p)
REVERT: S   76 LYS cc_start: 0.7370 (mtpp) cc_final: 0.6994 (ttmt)
REVERT: S  186 GLN cc_start: 0.7570 (tt0) cc_final: 0.7345 (tt0)
  outliers start: 46
  outliers final: 24
  residues processed: 164
  average time/residue: 1.2164
  time to fit residues: 212.7738
Evaluate side-chains
  160 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  166 MET
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 104 optimal weight:    0.4980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 ASN
A  52 GLN
A 204 GLN
B 340 ASN
G  18 GLN
G  59 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          1.0797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9425  Z= 0.140
  Angle     :  0.484   7.156  12797  Z= 0.251
  Chirality :  0.040   0.138   1457
  Planarity :  0.003   0.053   1586
  Dihedral  :  5.393  57.203   1574
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 21.05 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.86 (0.25), residues: 1144
  helix:  2.21 (0.28), residues: 389
  sheet:  0.21 (0.30), residues: 279
  loop : -0.57 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.018   0.001   PHE R 115 
 TYR   0.009   0.001   TYR S 190 
 ARG   0.005   0.000   ARG S 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 134
  time to evaluate  : 0.944 
Fit side-chains
REVERT: R  234 MET cc_start: 0.7360 (mmm) cc_final: 0.7079 (mmp)
REVERT: R  252 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6711 (m)
REVERT: A   17 LYS cc_start: 0.6252 (mttt) cc_final: 0.5909 (mtmt)
REVERT: A   22 ASN cc_start: 0.6815 (m-40) cc_final: 0.6564 (m110)
REVERT: A   25 GLU cc_start: 0.6149 (tt0) cc_final: 0.5817 (tt0)
REVERT: A   28 GLU cc_start: 0.6962 (tt0) cc_final: 0.6460 (mt-10)
REVERT: A  209 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7102 (mmtm)
REVERT: A  229 ASP cc_start: 0.6813 (m-30) cc_final: 0.6376 (p0)
REVERT: A  251 ASP cc_start: 0.7580 (t70) cc_final: 0.7344 (t0)
REVERT: B   32 GLN cc_start: 0.8207 (mt0) cc_final: 0.7999 (mt0)
REVERT: B   42 ARG cc_start: 0.6321 (tpt170) cc_final: 0.5893 (tmt170)
REVERT: B  130 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6060 (mp0)
REVERT: B  134 ARG cc_start: 0.7260 (mtp180) cc_final: 0.6927 (ptp90)
REVERT: B  137 ARG cc_start: 0.6861 (mmp80) cc_final: 0.6515 (tpt170)
REVERT: B  172 GLU cc_start: 0.6923 (tp30) cc_final: 0.6551 (mt-10)
REVERT: B  212 ASP cc_start: 0.7755 (t0) cc_final: 0.7490 (t70)
REVERT: B  215 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7177 (mt-10)
REVERT: B  226 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7639 (pm20)
REVERT: B  296 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7646 (p)
REVERT: B  312 ASP cc_start: 0.7687 (m-30) cc_final: 0.7306 (m-30)
REVERT: S   46 GLU cc_start: 0.7933 (pt0) cc_final: 0.7294 (pt0)
REVERT: S   65 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6821 (ttpt)
REVERT: S   71 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7091 (p)
REVERT: S  118 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7345 (p)
REVERT: S  160 ARG cc_start: 0.7223 (ptt90) cc_final: 0.6098 (mtm-85)
REVERT: S  186 GLN cc_start: 0.7592 (tt0) cc_final: 0.7367 (tt0)
  outliers start: 41
  outliers final: 17
  residues processed: 157
  average time/residue: 1.2059
  time to fit residues: 201.9899
Evaluate side-chains
  151 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 ASN
A  52 GLN
A 204 GLN
B  16 ASN
B 340 ASN
G  18 GLN
G  59 ASN
S  77 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          1.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9425  Z= 0.181
  Angle     :  0.531   8.394  12797  Z= 0.272
  Chirality :  0.041   0.145   1457
  Planarity :  0.004   0.053   1586
  Dihedral  :  5.480  58.686   1574
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 20.85 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.88 (0.26), residues: 1144
  helix:  2.20 (0.27), residues: 389
  sheet:  0.20 (0.30), residues: 282
  loop : -0.52 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.021   0.001   PHE R 115 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 135
  time to evaluate  : 1.004 
Fit side-chains
REVERT: R  193 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.4856 (p0)
REVERT: R  234 MET cc_start: 0.7343 (mmm) cc_final: 0.7092 (mmp)
REVERT: R  252 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6812 (m)
REVERT: R  308 GLU cc_start: 0.7450 (mp0) cc_final: 0.6457 (tp30)
REVERT: A   17 LYS cc_start: 0.6238 (mttt) cc_final: 0.5897 (mtmt)
REVERT: A   22 ASN cc_start: 0.6862 (m-40) cc_final: 0.6617 (m110)
REVERT: A   25 GLU cc_start: 0.6139 (tt0) cc_final: 0.5830 (tt0)
REVERT: A   28 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6467 (mt-10)
REVERT: A  198 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7802 (ttm)
REVERT: A  209 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7138 (mptt)
REVERT: A  229 ASP cc_start: 0.6808 (m-30) cc_final: 0.6438 (p0)
REVERT: A  251 ASP cc_start: 0.7714 (t70) cc_final: 0.7437 (t0)
REVERT: A  272 ASP cc_start: 0.6539 (m-30) cc_final: 0.6335 (m-30)
REVERT: B   32 GLN cc_start: 0.8192 (mt0) cc_final: 0.7991 (mt0)
REVERT: B   42 ARG cc_start: 0.6347 (tpt170) cc_final: 0.5917 (tmt170)
REVERT: B  130 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6038 (mp0)
REVERT: B  134 ARG cc_start: 0.7276 (mtp180) cc_final: 0.6950 (ptp90)
REVERT: B  137 ARG cc_start: 0.7029 (mmp80) cc_final: 0.6569 (tpt170)
REVERT: B  226 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7578 (pm20)
REVERT: B  312 ASP cc_start: 0.7699 (m-30) cc_final: 0.7317 (m-30)
REVERT: G   58 GLU cc_start: 0.6720 (mt-10) cc_final: 0.5619 (tm-30)
REVERT: S   46 GLU cc_start: 0.7975 (pt0) cc_final: 0.7343 (pt0)
REVERT: S   65 LYS cc_start: 0.7266 (ttmt) cc_final: 0.6934 (ttpt)
REVERT: S   71 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7122 (p)
REVERT: S  118 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7300 (p)
REVERT: S  140 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6637 (mmm)
REVERT: S  186 GLN cc_start: 0.7640 (tt0) cc_final: 0.7384 (tt0)
  outliers start: 44
  outliers final: 29
  residues processed: 158
  average time/residue: 1.1619
  time to fit residues: 196.5230
Evaluate side-chains
  171 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  166 MET
Chi-restraints excluded: chain R residue  193 ASP
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0070
   chunk 53 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    1.6604

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  47 ASN
A 204 GLN
A 322 HIS
B 340 ASN
G  18 GLN
G  59 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          1.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9425  Z= 0.237
  Angle     :  0.578   9.037  12797  Z= 0.296
  Chirality :  0.043   0.152   1457
  Planarity :  0.004   0.055   1586
  Dihedral  :  5.800  58.186   1574
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 21.36 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.76 (0.25), residues: 1144
  helix:  2.11 (0.27), residues: 389
  sheet:  0.11 (0.30), residues: 284
  loop : -0.58 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 211 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.027   0.002   PHE R 115 
 TYR   0.015   0.002   TYR S 190 
 ARG   0.007   0.001   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 136
  time to evaluate  : 1.014 
Fit side-chains
REVERT: R  234 MET cc_start: 0.7240 (mmm) cc_final: 0.7003 (mmp)
REVERT: R  252 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6873 (m)
REVERT: R  308 GLU cc_start: 0.7420 (mp0) cc_final: 0.6441 (tp30)
REVERT: A   17 LYS cc_start: 0.6290 (mttt) cc_final: 0.5943 (mtmt)
REVERT: A   22 ASN cc_start: 0.6876 (m-40) cc_final: 0.6628 (m110)
REVERT: A   25 GLU cc_start: 0.6123 (tt0) cc_final: 0.5563 (tm-30)
REVERT: A   28 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6533 (mt-10)
REVERT: A  198 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7861 (ttm)
REVERT: A  209 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7169 (mptt)
REVERT: A  251 ASP cc_start: 0.7871 (t70) cc_final: 0.7624 (t0)
REVERT: A  273 LEU cc_start: 0.7291 (tp) cc_final: 0.7012 (tp)
REVERT: B   32 GLN cc_start: 0.8050 (mt0) cc_final: 0.7788 (mt0)
REVERT: B   42 ARG cc_start: 0.6341 (tpt170) cc_final: 0.5914 (tmt170)
REVERT: B  130 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6016 (mp0)
REVERT: B  134 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6970 (ptp90)
REVERT: B  137 ARG cc_start: 0.7154 (mmp80) cc_final: 0.6551 (tpt170)
REVERT: B  172 GLU cc_start: 0.7059 (tp30) cc_final: 0.6854 (pt0)
REVERT: B  226 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7572 (pm20)
REVERT: B  312 ASP cc_start: 0.7657 (m-30) cc_final: 0.7297 (m-30)
REVERT: G   58 GLU cc_start: 0.6773 (mt-10) cc_final: 0.5798 (tm-30)
REVERT: S   46 GLU cc_start: 0.8002 (pt0) cc_final: 0.7381 (pt0)
REVERT: S   65 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6917 (ttpt)
REVERT: S   71 SER cc_start: 0.7339 (OUTLIER) cc_final: 0.6994 (p)
REVERT: S   76 LYS cc_start: 0.7318 (mtpp) cc_final: 0.6859 (ttmt)
REVERT: S  140 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6659 (mmm)
REVERT: S  186 GLN cc_start: 0.7664 (tt0) cc_final: 0.7379 (tt0)
  outliers start: 48
  outliers final: 29
  residues processed: 166
  average time/residue: 1.1141
  time to fit residues: 198.5426
Evaluate side-chains
  166 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  132 ASP
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  166 MET
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 103 optimal weight:    0.0050
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.0998

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  36 ASN
B 340 ASN
G  18 GLN
G  59 ASN
S  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          1.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9425  Z= 0.178
  Angle     :  0.534   9.148  12797  Z= 0.272
  Chirality :  0.041   0.142   1457
  Planarity :  0.004   0.055   1586
  Dihedral  :  5.584  56.038   1574
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.47 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.89 (0.25), residues: 1144
  helix:  2.27 (0.27), residues: 389
  sheet:  0.19 (0.30), residues: 277
  loop : -0.56 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.023   0.001   PHE R 115 
 TYR   0.014   0.001   TYR S 190 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 1.114 
Fit side-chains
REVERT: R  118 SER cc_start: 0.8379 (m) cc_final: 0.7981 (p)
REVERT: R  234 MET cc_start: 0.7265 (mmm) cc_final: 0.7038 (mmp)
REVERT: R  252 VAL cc_start: 0.7069 (OUTLIER) cc_final: 0.6812 (m)
REVERT: R  308 GLU cc_start: 0.7467 (mp0) cc_final: 0.7203 (mt-10)
REVERT: A   17 LYS cc_start: 0.6239 (mttt) cc_final: 0.5895 (mtmt)
REVERT: A   22 ASN cc_start: 0.6823 (m-40) cc_final: 0.6591 (m110)
REVERT: A   25 GLU cc_start: 0.6161 (tt0) cc_final: 0.5813 (tt0)
REVERT: A   28 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6466 (mt-10)
REVERT: A  198 MET cc_start: 0.8093 (mtm) cc_final: 0.7820 (ttp)
REVERT: A  209 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7166 (mptt)
REVERT: A  229 ASP cc_start: 0.6765 (m-30) cc_final: 0.6431 (p0)
REVERT: A  251 ASP cc_start: 0.7789 (t70) cc_final: 0.7579 (t0)
REVERT: A  273 LEU cc_start: 0.7207 (tp) cc_final: 0.6941 (tp)
REVERT: B   32 GLN cc_start: 0.8061 (mt0) cc_final: 0.7859 (mt0)
REVERT: B   42 ARG cc_start: 0.6307 (tpt170) cc_final: 0.5642 (tmt170)
REVERT: B  130 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6025 (mp0)
REVERT: B  134 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6969 (ptp90)
REVERT: B  137 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6491 (tpt170)
REVERT: B  172 GLU cc_start: 0.7063 (tp30) cc_final: 0.6830 (pt0)
REVERT: B  226 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7474 (pm20)
REVERT: B  312 ASP cc_start: 0.7725 (m-30) cc_final: 0.7360 (m-30)
REVERT: G   58 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5643 (tm-30)
REVERT: S   46 GLU cc_start: 0.8025 (pt0) cc_final: 0.7400 (pt0)
REVERT: S   65 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6961 (ttpt)
REVERT: S   71 SER cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (p)
REVERT: S   76 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6805 (ttmt)
REVERT: S  118 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7180 (p)
REVERT: S  186 GLN cc_start: 0.7644 (tt0) cc_final: 0.7378 (tt0)
  outliers start: 41
  outliers final: 26
  residues processed: 158
  average time/residue: 1.1049
  time to fit residues: 187.3794
Evaluate side-chains
  165 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 111 optimal weight:    0.8980
   chunk 102 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  36 ASN
B 340 ASN
G  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          1.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9425  Z= 0.156
  Angle     :  0.519   9.081  12797  Z= 0.263
  Chirality :  0.040   0.141   1457
  Planarity :  0.003   0.054   1586
  Dihedral  :  5.432  58.032   1574
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.08 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.99 (0.26), residues: 1144
  helix:  2.39 (0.27), residues: 389
  sheet:  0.22 (0.30), residues: 276
  loop : -0.51 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.019   0.001   PHE R 115 
 TYR   0.023   0.001   TYR R 293 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.148 
Fit side-chains
REVERT: R  118 SER cc_start: 0.8372 (m) cc_final: 0.7991 (p)
REVERT: R  234 MET cc_start: 0.7251 (mmm) cc_final: 0.7012 (mmp)
REVERT: R  252 VAL cc_start: 0.7019 (OUTLIER) cc_final: 0.6802 (m)
REVERT: R  271 GLU cc_start: 0.7486 (tp30) cc_final: 0.7079 (mm-30)
REVERT: R  308 GLU cc_start: 0.7465 (mp0) cc_final: 0.7199 (mt-10)
REVERT: A   17 LYS cc_start: 0.6211 (mttt) cc_final: 0.5869 (mtmt)
REVERT: A   22 ASN cc_start: 0.6804 (m-40) cc_final: 0.6574 (m110)
REVERT: A   25 GLU cc_start: 0.6150 (tt0) cc_final: 0.5817 (tt0)
REVERT: A   28 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6457 (mt-10)
REVERT: A  209 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7181 (mppt)
REVERT: A  229 ASP cc_start: 0.6737 (m-30) cc_final: 0.6419 (p0)
REVERT: A  251 ASP cc_start: 0.7746 (t70) cc_final: 0.7498 (t0)
REVERT: A  273 LEU cc_start: 0.7195 (tp) cc_final: 0.6927 (tp)
REVERT: B   32 GLN cc_start: 0.8076 (mt0) cc_final: 0.7841 (mt0)
REVERT: B   42 ARG cc_start: 0.6316 (tpt170) cc_final: 0.5666 (tmt170)
REVERT: B  130 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6081 (mp0)
REVERT: B  137 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6489 (tpt170)
REVERT: B  172 GLU cc_start: 0.7091 (tp30) cc_final: 0.6762 (pt0)
REVERT: B  212 ASP cc_start: 0.7721 (t0) cc_final: 0.7376 (t70)
REVERT: B  226 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7448 (pm20)
REVERT: B  296 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7665 (p)
REVERT: B  312 ASP cc_start: 0.7684 (m-30) cc_final: 0.7363 (m-30)
REVERT: G   58 GLU cc_start: 0.6686 (mt-10) cc_final: 0.5789 (tm-30)
REVERT: S   46 GLU cc_start: 0.7939 (pt0) cc_final: 0.7384 (pt0)
REVERT: S   65 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6576 (tttm)
REVERT: S   71 SER cc_start: 0.7411 (OUTLIER) cc_final: 0.7090 (p)
REVERT: S   76 LYS cc_start: 0.7227 (mtpp) cc_final: 0.6786 (ttmt)
REVERT: S  118 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7199 (p)
REVERT: S  186 GLN cc_start: 0.7601 (tt0) cc_final: 0.7322 (tt0)
REVERT: L   11 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (mt)
  outliers start: 39
  outliers final: 26
  residues processed: 152
  average time/residue: 1.1467
  time to fit residues: 186.7428
Evaluate side-chains
  160 residues out of total 988 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  162 LEU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain L residue   11 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   chunk 88 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B  36 ASN
B 340 ASN
G  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.169107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.138306 restraints weight = 11210.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.87
r_work: 0.3478 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          1.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9425  Z= 0.144
  Angle     :  0.502   8.933  12797  Z= 0.258
  Chirality :  0.040   0.139   1457
  Planarity :  0.003   0.054   1586
  Dihedral  :  5.337  59.376   1574
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.87 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.08 (0.26), residues: 1144
  helix:  2.48 (0.27), residues: 390
  sheet:  0.21 (0.30), residues: 281
  loop : -0.45 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.015   0.001   PHE R 115 
 TYR   0.019   0.001   TYR R 293 
 ARG   0.004   0.000   ARG B 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3836.68 seconds
wall clock time: 68 minutes 10.53 seconds (4090.53 seconds total)