Starting phenix.real_space_refine
on Sat Aug  3 17:25:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/08_2024/8ykw_39374_neut.cif"
  }
  resolution = 2.75
  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=   0.001 sd=   0.081
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      55      5.16       5
     C    5574      2.51       5
     N    1481      2.21       5
     O    1608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "A GLU  297": "OE1" <-> "OE2"
    Residue "A GLU  298": "OE1" <-> "OE2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B GLU  260": "OE1" <-> "OE2"
    Residue "G GLU   22": "OE1" <-> "OE2"
    Residue "G GLU   42": "OE1" <-> "OE2"
    Residue "R GLU   33": "OE1" <-> "OE2"
    Residue "R PHE   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  153": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 8718
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1713
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2560
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 19
    Chain: "E"
      Number of atoms: 1719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1719
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "G"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 440
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2278
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 12, 'TRANS': 271}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SIN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.82, per 1000 atoms: 0.55
  Number of scatterers: 8718
  At special positions: 0
  Unit cell: (86.1, 119.72, 135.3, 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      55     16.00
     O    1608      8.00
     N    1481      7.00
     C    5574      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 268 " distance=2.30

  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: 3.40
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      39.2% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.746A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.407A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.161A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.951A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.701A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 11 through 24
    Processing helix  chain 'R' and resid 24 through 49
    Processing helix  chain 'R' and resid 56 through 74
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.008A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
      removed outlier: 3.664A  pdb=" N   ILE R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 131 through 134
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 180 through 196
      removed outlier: 3.603A  pdb=" N   ILE R 186 " --> pdb=" O   ASN R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 217
    Processing helix  chain 'R' and resid 227 through 260
      removed outlier: 3.563A  pdb=" N   VAL R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 3.534A  pdb=" N   ILE R 273 " --> pdb=" O   THR R 269 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL R 279 " --> pdb=" O   SER R 275 " (cutoff:3.500A)
      Proline residue:  R 282  - end of helix
    Processing helix  chain 'R' and resid 286 through 297
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.082A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.664A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.690A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.746A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.257A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.545A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.421A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.725A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.938A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.416A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.375A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.869A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1308 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: 2.70

  Time building geometry restraints manager: 3.66 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1410
        1.31 -     1.44: 2459
        1.44 -     1.57: 4948
        1.57 -     1.69: 2
        1.69 -     1.82: 78
  Bond restraints: 8897
  Sorted by residual:
  bond pdb=" CA  LEU E 233 "
       pdb=" C   LEU E 233 "
    ideal  model  delta    sigma   weight residual
    1.524  1.451  0.073 1.32e-02 5.74e+03 3.05e+01
  bond pdb=" CA  LEU E 237 "
       pdb=" C   LEU E 237 "
    ideal  model  delta    sigma   weight residual
    1.523  1.460  0.063 1.30e-02 5.92e+03 2.37e+01
  bond pdb=" CA  VAL A 233 "
       pdb=" C   VAL A 233 "
    ideal  model  delta    sigma   weight residual
    1.524  1.473  0.051 1.08e-02 8.57e+03 2.21e+01
  bond pdb=" CA  THR R 246 "
       pdb=" C   THR R 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.571 -0.049 1.17e-02 7.31e+03 1.77e+01
  bond pdb=" C   LEU E 237 "
       pdb=" O   LEU E 237 "
    ideal  model  delta    sigma   weight residual
    1.234  1.186  0.048 1.23e-02 6.61e+03 1.53e+01
  ... (remaining 8892 not shown)

  Histogram of bond angle deviations from ideal:
      100.42 -   107.59: 281
      107.59 -   114.75: 5199
      114.75 -   121.91: 4778
      121.91 -   129.08: 1741
      129.08 -   136.24: 62
  Bond angle restraints: 12061
  Sorted by residual:
  angle pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
        pdb=" CA  PRO R 230 "
      ideal   model   delta    sigma   weight residual
     119.05  111.98    7.07 1.11e+00 8.12e-01 4.06e+01
  angle pdb=" N   GLN R 270 "
        pdb=" CA  GLN R 270 "
        pdb=" C   GLN R 270 "
      ideal   model   delta    sigma   weight residual
     112.23  104.57    7.66 1.26e+00 6.30e-01 3.70e+01
  angle pdb=" N   LEU A 232 "
        pdb=" CA  LEU A 232 "
        pdb=" C   LEU A 232 "
      ideal   model   delta    sigma   weight residual
     110.55  102.91    7.64 1.35e+00 5.49e-01 3.20e+01
  angle pdb=" O   LYS R 229 "
        pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
      ideal   model   delta    sigma   weight residual
     120.48  124.76   -4.28 8.90e-01 1.26e+00 2.31e+01
  angle pdb=" CA  LYS R 229 "
        pdb=" C   LYS R 229 "
        pdb=" N   PRO R 230 "
      ideal   model   delta    sigma   weight residual
     120.77  116.60    4.17 9.70e-01 1.06e+00 1.85e+01
  ... (remaining 12056 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4725
       17.91 -    35.82: 410
       35.82 -    53.73: 107
       53.73 -    71.63: 14
       71.63 -    89.54: 8
  Dihedral angle restraints: 5264
    sinusoidal: 1998
      harmonic: 3266
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.72   19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1182
       0.055 -    0.109: 156
       0.109 -    0.164: 37
       0.164 -    0.219: 1
       0.219 -    0.273: 4
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CA  TYR E 235 "
            pdb=" N   TYR E 235 "
            pdb=" C   TYR E 235 "
            pdb=" CB  TYR E 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  ILE R 278 "
            pdb=" N   ILE R 278 "
            pdb=" C   ILE R 278 "
            pdb=" CB  ILE R 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  THR E 238 "
            pdb=" N   THR E 238 "
            pdb=" C   THR E 238 "
            pdb=" CB  THR E 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1377 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 150 "    0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO E 151 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E 151 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 151 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 245 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   PHE R 245 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PHE R 245 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR R 246 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 291 "   -0.037 5.00e-02 4.00e+02   5.59e-02 4.99e+00
        pdb=" N   PRO R 292 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO R 292 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 292 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1688
        2.77 -     3.30: 8501
        3.30 -     3.84: 14751
        3.84 -     4.37: 18209
        4.37 -     4.90: 31450
  Nonbonded interactions: 74599
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ASN R 274 "
            pdb=" N   TYR R 277 "
     model   vdw
     2.313 3.120
  ... (remaining 74594 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.190
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:11.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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      :  0.004   0.073   8897  Z= 0.252
  Angle     :  0.652  11.238  12061  Z= 0.374
  Chirality :  0.043   0.273   1380
  Planarity :  0.005   0.068   1523
  Dihedral  : 14.747  89.543   3153
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 15.09 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1100
  helix:  1.71 (0.27), residues: 383
  sheet:  0.32 (0.29), residues: 307
  loop :  0.27 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  88 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R  34 
 TYR   0.016   0.001   TYR R  83 
 ARG   0.014   0.001   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: B   46 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7854 (ptm160)
REVERT: B  219 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7352 (mmt-90)
REVERT: E   46 GLU cc_start: 0.8026 (tt0) cc_final: 0.7812 (tt0)
REVERT: R  189 MET cc_start: 0.8267 (mmm) cc_final: 0.8018 (mmm)
  outliers start: 5
  outliers final: 2
  residues processed: 146
  average time/residue: 1.3001
  time to fit residues: 201.2855
Evaluate side-chains
  121 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain E residue  193 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
A 269 ASN
A 331 ASN
A 333 GLN
B  75 GLN
B 259 GLN
E  77 ASN
E 179 GLN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8897  Z= 0.213
  Angle     :  0.558   9.305  12061  Z= 0.300
  Chirality :  0.043   0.153   1380
  Planarity :  0.004   0.039   1523
  Dihedral  :  4.602  37.606   1221
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.66 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1100
  helix:  2.31 (0.25), residues: 388
  sheet:  0.43 (0.31), residues: 293
  loop :  0.47 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.014   0.001   PHE A 274 
 TYR   0.022   0.001   TYR R  48 
 ARG   0.007   0.001   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8227 (tt0) cc_final: 0.7844 (tt0)
REVERT: B  214 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7810 (mmp80)
REVERT: B  219 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7286 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7765 (m-30) cc_final: 0.7444 (m-30)
REVERT: E   46 GLU cc_start: 0.8034 (tt0) cc_final: 0.7807 (tt0)
REVERT: E  229 CYS cc_start: 0.8429 (p) cc_final: 0.8165 (p)
REVERT: R  189 MET cc_start: 0.8433 (mmm) cc_final: 0.8042 (mmm)
REVERT: R  193 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7615 (tt)
REVERT: R  253 ASN cc_start: 0.8743 (m-40) cc_final: 0.8382 (m-40)
  outliers start: 24
  outliers final: 9
  residues processed: 151
  average time/residue: 1.2113
  time to fit residues: 194.6736
Evaluate side-chains
  129 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 89 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
A 331 ASN
B  75 GLN
B 259 GLN
E  39 GLN
E  77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8897  Z= 0.401
  Angle     :  0.615   9.791  12061  Z= 0.327
  Chirality :  0.046   0.162   1380
  Planarity :  0.004   0.038   1523
  Dihedral  :  4.577  21.267   1218
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 15.52 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1100
  helix:  2.24 (0.25), residues: 388
  sheet:  0.41 (0.30), residues: 293
  loop :  0.28 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.006   0.001   HIS G  44 
 PHE   0.016   0.002   PHE R 115 
 TYR   0.019   0.002   TYR R  48 
 ARG   0.007   0.001   ARG E 160 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8236 (tt0) cc_final: 0.7878 (tt0)
REVERT: B  219 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7184 (mmt180)
REVERT: E   46 GLU cc_start: 0.8128 (tt0) cc_final: 0.7903 (tt0)
REVERT: E  183 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (mt0)
REVERT: E  244 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8082 (tttm)
REVERT: R  189 MET cc_start: 0.8494 (mmm) cc_final: 0.8090 (mmm)
REVERT: R  193 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (tt)
REVERT: R  253 ASN cc_start: 0.8769 (m-40) cc_final: 0.8413 (m-40)
  outliers start: 39
  outliers final: 17
  residues processed: 153
  average time/residue: 1.1746
  time to fit residues: 191.9294
Evaluate side-chains
  143 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  293 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    9.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
A 331 ASN
B  75 GLN
B 237 ASN
B 239 ASN
B 259 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8897  Z= 0.218
  Angle     :  0.542   9.790  12061  Z= 0.288
  Chirality :  0.043   0.155   1380
  Planarity :  0.004   0.042   1523
  Dihedral  :  4.303  21.961   1218
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.92 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1100
  helix:  2.48 (0.25), residues: 388
  sheet:  0.45 (0.30), residues: 291
  loop :  0.22 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.010   0.001   HIS B 266 
 PHE   0.018   0.001   PHE A 274 
 TYR   0.023   0.001   TYR R  48 
 ARG   0.004   0.000   ARG B 314 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 1.061 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8220 (tt0) cc_final: 0.7864 (tt0)
REVERT: B  219 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7200 (mmt180)
REVERT: E   46 GLU cc_start: 0.8102 (tt0) cc_final: 0.7893 (tt0)
REVERT: E  244 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8135 (tttm)
REVERT: R  189 MET cc_start: 0.8509 (mmm) cc_final: 0.8087 (mmm)
REVERT: R  253 ASN cc_start: 0.8741 (m-40) cc_final: 0.8404 (m-40)
  outliers start: 33
  outliers final: 18
  residues processed: 152
  average time/residue: 1.1419
  time to fit residues: 185.5671
Evaluate side-chains
  143 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  234 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0870
   chunk 1 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 90 optimal weight:    0.4980
   chunk 73 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
B 259 GLN
E  77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8897  Z= 0.170
  Angle     :  0.524  10.473  12061  Z= 0.276
  Chirality :  0.041   0.160   1380
  Planarity :  0.004   0.055   1523
  Dihedral  :  4.057  20.965   1218
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.00 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1100
  helix:  2.63 (0.25), residues: 388
  sheet:  0.44 (0.30), residues: 291
  loop :  0.24 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.008   0.001   HIS B 266 
 PHE   0.019   0.001   PHE A 274 
 TYR   0.025   0.001   TYR R  48 
 ARG   0.004   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8276 (tt0) cc_final: 0.7915 (tt0)
REVERT: B  219 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7265 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7838 (m-30) cc_final: 0.7568 (m-30)
REVERT: E   46 GLU cc_start: 0.8097 (tt0) cc_final: 0.7860 (tt0)
REVERT: E  229 CYS cc_start: 0.8432 (p) cc_final: 0.8219 (p)
REVERT: E  244 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8161 (tttm)
REVERT: R  189 MET cc_start: 0.8482 (mmm) cc_final: 0.8023 (mmm)
REVERT: R  193 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (tt)
REVERT: R  253 ASN cc_start: 0.8775 (m-40) cc_final: 0.8415 (m-40)
  outliers start: 25
  outliers final: 14
  residues processed: 153
  average time/residue: 1.1900
  time to fit residues: 194.3948
Evaluate side-chains
  144 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 21 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
B 259 GLN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8897  Z= 0.293
  Angle     :  0.576   8.871  12061  Z= 0.301
  Chirality :  0.044   0.223   1380
  Planarity :  0.004   0.055   1523
  Dihedral  :  4.288  21.247   1218
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.07 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.25), residues: 1100
  helix:  2.55 (0.25), residues: 388
  sheet:  0.45 (0.30), residues: 293
  loop :  0.17 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.014   0.002   PHE A 196 
 TYR   0.026   0.001   TYR R  48 
 ARG   0.006   0.001   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.8289 (tt0) cc_final: 0.7950 (tt0)
REVERT: B  153 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7701 (p0)
REVERT: B  219 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7225 (mmt180)
REVERT: B  267 ASP cc_start: 0.7893 (m-30) cc_final: 0.7661 (m-30)
REVERT: E   46 GLU cc_start: 0.8123 (tt0) cc_final: 0.7894 (tt0)
REVERT: E  160 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7664 (mmm-85)
REVERT: E  183 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8122 (mt0)
REVERT: E  244 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8171 (tttm)
REVERT: R  193 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7846 (tt)
REVERT: R  253 ASN cc_start: 0.8808 (m-40) cc_final: 0.8549 (m-40)
  outliers start: 31
  outliers final: 20
  residues processed: 148
  average time/residue: 1.1730
  time to fit residues: 185.4688
Evaluate side-chains
  147 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   98 ASN
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  234 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 89 optimal weight:    0.2980
   chunk 59 optimal weight:    0.5980
   chunk 106 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 331 ASN
B  75 GLN
E  77 ASN
R 134 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8897  Z= 0.168
  Angle     :  0.531   8.716  12061  Z= 0.277
  Chirality :  0.042   0.169   1380
  Planarity :  0.004   0.040   1523
  Dihedral  :  4.045  22.277   1218
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.15 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.26), residues: 1100
  helix:  2.65 (0.25), residues: 389
  sheet:  0.42 (0.30), residues: 283
  loop :  0.15 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.009   0.001   PHE R 115 
 TYR   0.028   0.001   TYR R  48 
 ARG   0.005   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.8054 (mpt90) cc_final: 0.7834 (mpt90)
REVERT: B  153 ASP cc_start: 0.8075 (m-30) cc_final: 0.7845 (p0)
REVERT: B  219 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7222 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7781 (m-30) cc_final: 0.7527 (m-30)
REVERT: E  160 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7581 (tpp-160)
REVERT: E  229 CYS cc_start: 0.8437 (p) cc_final: 0.8232 (p)
REVERT: E  244 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8199 (tttm)
REVERT: R  217 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7657 (ttm170)
REVERT: R  253 ASN cc_start: 0.8809 (m-40) cc_final: 0.8542 (m-40)
  outliers start: 21
  outliers final: 12
  residues processed: 146
  average time/residue: 1.1662
  time to fit residues: 181.8813
Evaluate side-chains
  137 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   98 ASN
Chi-restraints excluded: chain R residue  217 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 20 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0370
   chunk 72 optimal weight:    5.9990
   chunk 52 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 96 optimal weight:    0.1980
   chunk 101 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.2268

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   8897  Z= 0.140
  Angle     :  0.513   8.300  12061  Z= 0.267
  Chirality :  0.041   0.161   1380
  Planarity :  0.003   0.040   1523
  Dihedral  :  3.904  22.351   1218
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.55 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.26), residues: 1100
  helix:  2.81 (0.25), residues: 389
  sheet:  0.46 (0.30), residues: 282
  loop :  0.20 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.015   0.001   PHE A 274 
 TYR   0.030   0.001   TYR R  48 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7904 (mpt90) cc_final: 0.7672 (mpt90)
REVERT: A  298 GLU cc_start: 0.8275 (tt0) cc_final: 0.7998 (tt0)
REVERT: B  219 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7207 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7711 (m-30) cc_final: 0.7430 (m-30)
REVERT: E  160 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7557 (tpp-160)
REVERT: E  244 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8108 (tttm)
REVERT: R  193 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (tt)
REVERT: R  253 ASN cc_start: 0.8781 (m-40) cc_final: 0.8514 (m-40)
  outliers start: 15
  outliers final: 11
  residues processed: 143
  average time/residue: 1.1374
  time to fit residues: 173.6501
Evaluate side-chains
  138 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   98 ASN
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 89 optimal weight:    8.9990
   chunk 93 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 259 GLN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8897  Z= 0.194
  Angle     :  0.547   8.248  12061  Z= 0.282
  Chirality :  0.042   0.190   1380
  Planarity :  0.003   0.039   1523
  Dihedral  :  3.997  22.196   1218
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.55 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1100
  helix:  2.82 (0.25), residues: 388
  sheet:  0.48 (0.31), residues: 279
  loop :  0.19 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.011   0.001   PHE R  34 
 TYR   0.015   0.001   TYR R 248 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7966 (mpt90) cc_final: 0.7732 (mpt90)
REVERT: B  219 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7215 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7753 (m-30) cc_final: 0.7490 (m-30)
REVERT: E  160 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7586 (tpp-160)
REVERT: E  244 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8081 (tttm)
REVERT: R  193 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7968 (tt)
REVERT: R  253 ASN cc_start: 0.8788 (m-40) cc_final: 0.8530 (m-40)
  outliers start: 18
  outliers final: 14
  residues processed: 139
  average time/residue: 1.1497
  time to fit residues: 170.9014
Evaluate side-chains
  140 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0770
   chunk 109 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0870
   chunk 67 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  75 GLN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.073   8897  Z= 0.163
  Angle     :  0.526   8.512  12061  Z= 0.273
  Chirality :  0.041   0.177   1380
  Planarity :  0.003   0.039   1523
  Dihedral  :  3.913  22.107   1218
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.77 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1100
  helix:  2.87 (0.25), residues: 388
  sheet:  0.44 (0.30), residues: 286
  loop :  0.25 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.009   0.001   PHE A 196 
 TYR   0.015   0.001   TYR R 248 
 ARG   0.007   0.000   ARG R 255 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7865 (mpt90) cc_final: 0.7630 (mpt90)
REVERT: A  298 GLU cc_start: 0.8277 (tt0) cc_final: 0.8009 (tt0)
REVERT: B  219 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7211 (mmt-90)
REVERT: B  267 ASP cc_start: 0.7677 (m-30) cc_final: 0.7419 (m-30)
REVERT: E  160 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7621 (tpp-160)
REVERT: E  244 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8104 (tttm)
REVERT: R   64 ASN cc_start: 0.7958 (m110) cc_final: 0.7633 (m-40)
REVERT: R  193 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: R  253 ASN cc_start: 0.8761 (m-40) cc_final: 0.8491 (m-40)
  outliers start: 20
  outliers final: 13
  residues processed: 137
  average time/residue: 1.1224
  time to fit residues: 164.9194
Evaluate side-chains
  140 residues out of total 971 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0570
   chunk 89 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.0700

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111084 restraints weight = 9942.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.42
r_work: 0.3161 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8897  Z= 0.216
  Angle     :  0.559   8.413  12061  Z= 0.289
  Chirality :  0.042   0.166   1380
  Planarity :  0.004   0.037   1523
  Dihedral  :  4.024  22.157   1218
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 22.63 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.26), residues: 1100
  helix:  2.82 (0.25), residues: 387
  sheet:  0.40 (0.30), residues: 287
  loop :  0.23 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.015   0.001   TYR R 248 
 ARG   0.007   0.000   ARG R 255 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3711.85 seconds
wall clock time: 65 minutes 39.33 seconds (3939.33 seconds total)