Starting phenix.real_space_refine
on Thu Jan 16 05:01:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xgs_38331/01_2025/8xgs_38331.cif"
  }
  resolution = 2.95
  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=   0.011
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      59      5.16       5
     C    5724      2.51       5
     N    1558      2.21       5
     O    1655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8996
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2274
          Classifications: {'peptide': 294}
          Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 276}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2559
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "D"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1791
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1880
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 73
          Classifications: {'peptide': 8}
          Link IDs: {'CIS': 1, 'TRANS': 6}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.61
  Number of scatterers: 8996
  At special positions: 0
  Unit cell: (89.25, 124.95, 131.75, 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      59     16.00
     O    1655      8.00
     N    1558      7.00
     C    5724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 191 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  39 " - pdb=" SG  CYS D 113 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  ASN F   2 "
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      36.3% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 70
      Proline residue:  A  46  - end of helix
      removed outlier: 3.563A  pdb=" N   HIS A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 83
    Processing helix  chain 'A' and resid 85 through 102
      Proline residue:  A  97  - end of helix
      removed outlier: 3.726A  pdb=" N   LEU A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 146
      removed outlier: 3.690A  pdb=" N   CYS A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS A 116 " --> pdb=" O   ASP A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.609A  pdb=" N   ALA A 179 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 213
    Processing helix  chain 'A' and resid 213 through 223
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 3.604A  pdb=" N   VAL A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 287
      removed outlier: 3.727A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
    Processing helix  chain 'A' and resid 298 through 325
      removed outlier: 3.839A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA A 317 " --> pdb=" O   TYR A 313 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'A' and resid 327 through 336
      removed outlier: 3.973A  pdb=" N   ARG A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 49
      removed outlier: 3.524A  pdb=" N   SER D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 82
    Processing helix  chain 'D' and resid 104 through 108
    Processing helix  chain 'E' and resid 8 through 30
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 210 through 215
      removed outlier: 3.604A  pdb=" N   CYS E 213 " --> pdb=" O   TRP E 210 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 229
      No H-bonds generated for 'chain 'E' and resid 227 through 229'
    Processing helix  chain 'E' and resid 240 through 247
    Processing helix  chain 'E' and resid 249 through 254
    Processing helix  chain 'E' and resid 255 through 261
      removed outlier: 3.597A  pdb=" N   GLN E 259 " --> pdb=" O   PRO E 256 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   ASN E 260 " --> pdb=" O   TRP E 257 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER E 261 " --> pdb=" O   PHE E 258 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 275
    Processing helix  chain 'E' and resid 297 through 309
    Processing helix  chain 'E' and resid 329 through 350
      removed outlier: 3.609A  pdb=" N   TYR E 350 " --> pdb=" O   ASN E 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.818A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 63
      removed outlier: 3.667A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.526A  pdb=" N   CYS B 114 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.548A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.668A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.472A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.170A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 24
    Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 29
      removed outlier: 5.880A  pdb=" N   GLY D  27 " --> pdb=" O   THR D 135 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 67 through 68
    Processing sheet with id=AB2, first strand: chain 'D' and resid 55 through 56
    Processing sheet with id=AB3, first strand: chain 'D' and resid 157 through 158
      removed outlier: 3.622A  pdb=" N   VAL D 172 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE D 229 " --> pdb=" O   CYS D 176 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR D 230 " --> pdb=" O   SER D 223 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER D 223 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 164
      removed outlier: 3.654A  pdb=" N   VAL D 164 " --> pdb=" O   LYS D 261 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE D 206 " --> pdb=" O   TRP D 193 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LEU D 195 " --> pdb=" O   LEU D 204 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   LEU D 204 " --> pdb=" O   LEU D 195 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 189
      removed outlier: 3.597A  pdb=" N   LEU E  34 " --> pdb=" O   ILE E 194 " (cutoff:3.500A)
      removed outlier: 9.698A  pdb=" N   SER E 219 " --> pdb=" O   GLU E  33 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LYS E  35 " --> pdb=" O   SER E 219 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   MET E 221 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU E  37 " --> pdb=" O   MET E 221 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   LEU E 223 " --> pdb=" O   LEU E  37 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   ILE E 220 " --> pdb=" O   ILE E 264 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   PHE E 266 " --> pdb=" O   ILE E 220 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   PHE E 222 " --> pdb=" O   PHE E 266 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ASN E 268 " --> pdb=" O   PHE E 222 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL E 224 " --> pdb=" O   ASN E 268 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   VAL E 263 " --> pdb=" O   TYR E 319 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1092 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: 2.65

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1444
        1.31 -     1.43: 2550
        1.43 -     1.56: 5108
        1.56 -     1.69: 3
        1.69 -     1.82: 87
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" C   SER F   3 "
       pdb=" N   PHE F   4 "
    ideal  model  delta    sigma   weight residual
    1.335  1.485 -0.150 1.25e-02 6.40e+03 1.45e+02
  bond pdb=" C   PHE F   4 "
       pdb=" N   GLY F   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.491 -0.162 1.40e-02 5.10e+03 1.35e+02
  bond pdb=" C   LEU F   6 "
       pdb=" N   ARG F   7 "
    ideal  model  delta    sigma   weight residual
    1.330  1.476 -0.146 1.31e-02 5.83e+03 1.24e+02
  bond pdb=" C   GLY F   5 "
       pdb=" N   LEU F   6 "
    ideal  model  delta    sigma   weight residual
    1.330  1.478 -0.148 1.41e-02 5.03e+03 1.10e+02
  bond pdb=" C   ARG F   7 "
       pdb=" N   PHE F   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.471 -0.142 1.40e-02 5.10e+03 1.03e+02
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 12238
        1.92 -     3.84: 186
        3.84 -     5.76: 34
        5.76 -     7.68: 6
        7.68 -     9.60: 2
  Bond angle restraints: 12466
  Sorted by residual:
  angle pdb=" CA  ASN F   2 "
        pdb=" CB  ASN F   2 "
        pdb=" CG  ASN F   2 "
      ideal   model   delta    sigma   weight residual
     112.60  118.69   -6.09 1.00e+00 1.00e+00 3.71e+01
  angle pdb=" CA  PHE F   4 "
        pdb=" C   PHE F   4 "
        pdb=" N   GLY F   5 "
      ideal   model   delta    sigma   weight residual
     116.97  122.85   -5.88 1.20e+00 6.94e-01 2.40e+01
  angle pdb=" CA  LEU F   6 "
        pdb=" C   LEU F   6 "
        pdb=" N   ARG F   7 "
      ideal   model   delta    sigma   weight residual
     115.36  120.83   -5.47 1.56e+00 4.11e-01 1.23e+01
  angle pdb=" CD  ARG F   7 "
        pdb=" NE  ARG F   7 "
        pdb=" CZ  ARG F   7 "
      ideal   model   delta    sigma   weight residual
     124.40  119.71    4.69 1.40e+00 5.10e-01 1.12e+01
  angle pdb=" CA  ARG F   7 "
        pdb=" C   ARG F   7 "
        pdb=" N   PHE F   8 "
      ideal   model   delta    sigma   weight residual
     115.51  119.69   -4.18 1.27e+00 6.20e-01 1.08e+01
  ... (remaining 12461 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 4952
       17.39 -    34.78: 415
       34.78 -    52.17: 64
       52.17 -    69.56: 13
       69.56 -    86.95: 8
  Dihedral angle restraints: 5452
    sinusoidal: 2115
      harmonic: 3337
  Sorted by residual:
  dihedral pdb=" CB  CYS D  39 "
           pdb=" SG  CYS D  39 "
           pdb=" SG  CYS D 113 "
           pdb=" CB  CYS D 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.79   49.79     1      1.00e+01 1.00e-02 3.40e+01
  dihedral pdb=" N   PHE F   8 "
           pdb=" C   PHE F   8 "
           pdb=" CA  PHE F   8 "
           pdb=" CB  PHE F   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.46  -12.66     0      2.50e+00 1.60e-01 2.57e+01
  dihedral pdb=" C   PHE F   8 "
           pdb=" N   PHE F   8 "
           pdb=" CA  PHE F   8 "
           pdb=" CB  PHE F   8 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.10   12.50     0      2.50e+00 1.60e-01 2.50e+01
  ... (remaining 5449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.009: 1403
       1.009 -    2.017: 0
       2.017 -    3.026: 0
       3.026 -    4.035: 0
       4.035 -    5.043: 1
  Chirality restraints: 1404
  Sorted by residual:
  chirality pdb=" CA  ASN F   2 "
            pdb=" N   ASN F   2 "
            pdb=" C   ASN F   2 "
            pdb=" CB  ASN F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.53    5.04 2.00e-01 2.50e+01 6.36e+02
  chirality pdb=" CA  PHE F   8 "
            pdb=" N   PHE F   8 "
            pdb=" C   PHE F   8 "
            pdb=" CB  PHE F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CA  ARG F   7 "
            pdb=" N   ARG F   7 "
            pdb=" C   ARG F   7 "
            pdb=" CB  ARG F   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.33e+00
  ... (remaining 1401 not shown)

  Planarity restraints: 1585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP E 271 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   ASP E 271 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASP E 271 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU E 272 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 184 "   -0.023 5.00e-02 4.00e+02   3.52e-02 1.99e+00
        pdb=" N   PRO A 185 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 229 "   -0.007 2.00e-02 2.50e+03   9.30e-03 1.51e+00
        pdb=" CG  PHE D 229 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 229 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 229 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 229 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 229 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1582 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 141
        2.66 -     3.22: 8435
        3.22 -     3.78: 13699
        3.78 -     4.34: 17856
        4.34 -     4.90: 30382
  Nonbonded interactions: 70513
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  47 "
            pdb=" OD1 ASP D  91 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   THR E  41 "
            pdb=" OG  SER E  44 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR A 213 "
            pdb=" O   ALA A 273 "
     model   vdw
     2.257 3.040
  ... (remaining 70508 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.300
  Find NCS groups from input model:        0.110
  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:13.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
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      :  0.006   0.162   9192  Z= 0.442
  Angle     :  0.607   9.601  12466  Z= 0.327
  Chirality :  0.142   5.043   1404
  Planarity :  0.003   0.035   1585
  Dihedral  : 13.203  86.954   3294
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.18 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.52 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.37 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.31 (0.26), residues: 1132
  helix:  1.71 (0.28), residues: 388
  sheet:  0.15 (0.34), residues: 252
  loop : -2.08 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  43 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.021   0.001   PHE D 229 
 TYR   0.017   0.001   TYR E 350 
 ARG   0.002   0.000   ARG A 229 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 1.046 
Fit side-chains
REVERT: C   48 ASP cc_start: 0.8469 (m-30) cc_final: 0.8246 (m-30)
REVERT: D   92 PRO cc_start: 0.8790 (Cg_exo) cc_final: 0.8486 (Cg_endo)
REVERT: D   93 LYS cc_start: 0.8523 (mppt) cc_final: 0.8284 (mppt)
REVERT: D  110 MET cc_start: 0.6586 (tmm) cc_final: 0.6316 (tmm)
REVERT: D  177 ARG cc_start: 0.8593 (mmm160) cc_final: 0.8309 (mmm160)
REVERT: D  237 GLU cc_start: 0.8485 (pm20) cc_final: 0.8190 (pm20)
REVERT: D  261 LYS cc_start: 0.8772 (tptp) cc_final: 0.8258 (tptt)
REVERT: D  263 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7834 (pm20)
REVERT: E  324 CYS cc_start: 0.8344 (p) cc_final: 0.7899 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 160
  average time/residue: 1.2067
  time to fit residues: 206.5425
Evaluate side-chains
  105 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    8 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0670
   chunk 101 optimal weight:    6.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.097028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073916 restraints weight = 20039.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.77
r_work: 0.3077 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9192  Z= 0.169
  Angle     :  0.642  10.700  12466  Z= 0.324
  Chirality :  0.049   0.933   1404
  Planarity :  0.004   0.036   1585
  Dihedral  :  4.452  34.692   1261
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.79 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1132
  helix:  1.78 (0.28), residues: 392
  sheet:  0.04 (0.34), residues: 256
  loop : -2.22 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.021   0.001   PHE D 229 
 TYR   0.012   0.001   TYR D 207 
 ARG   0.005   0.000   ARG E 204 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9010 (ptpp)
REVERT: B  262 MET cc_start: 0.8363 (tpp) cc_final: 0.8131 (tpp)
REVERT: C   48 ASP cc_start: 0.8401 (m-30) cc_final: 0.8102 (m-30)
REVERT: D   51 MET cc_start: 0.7598 (mmm) cc_final: 0.7351 (mmm)
REVERT: D   60 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8941 (mppt)
REVERT: D  110 MET cc_start: 0.6603 (tmm) cc_final: 0.6254 (tmm)
REVERT: D  177 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8791 (tpp-160)
REVERT: D  251 GLU cc_start: 0.9164 (pt0) cc_final: 0.8831 (pm20)
REVERT: D  261 LYS cc_start: 0.8603 (tptp) cc_final: 0.8083 (tptp)
REVERT: D  263 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7966 (pm20)
REVERT: E  350 TYR cc_start: 0.8339 (m-80) cc_final: 0.7568 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 137
  average time/residue: 1.1982
  time to fit residues: 176.0320
Evaluate side-chains
  117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain E residue   29 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0970
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 GLN
E 216 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.096898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.073715 restraints weight = 20273.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 3.78
r_work: 0.3074 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9192  Z= 0.168
  Angle     :  0.608   7.750  12466  Z= 0.308
  Chirality :  0.043   0.389   1404
  Planarity :  0.003   0.036   1585
  Dihedral  :  4.223  23.602   1259
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.41 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.28 (0.26), residues: 1132
  helix:  1.84 (0.28), residues: 398
  sheet:  0.04 (0.34), residues: 251
  loop : -2.15 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.000   HIS A 295 
 PHE   0.021   0.001   PHE D  85 
 TYR   0.020   0.001   TYR E 279 
 ARG   0.002   0.000   ARG B 214 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9010 (ptpp)
REVERT: B  215 GLU cc_start: 0.9050 (mp0) cc_final: 0.8714 (pm20)
REVERT: B  217 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.5998 (pp-130)
REVERT: B  262 MET cc_start: 0.8489 (tpp) cc_final: 0.8221 (tpp)
REVERT: C   46 LYS cc_start: 0.9560 (pmmt) cc_final: 0.9217 (pmtt)
REVERT: C   48 ASP cc_start: 0.8385 (m-30) cc_final: 0.8055 (m-30)
REVERT: D   51 MET cc_start: 0.7589 (mmm) cc_final: 0.7324 (mmm)
REVERT: D   75 ILE cc_start: 0.8957 (mm) cc_final: 0.8738 (mp)
REVERT: D  110 MET cc_start: 0.6839 (tmm) cc_final: 0.6328 (tmm)
REVERT: D  177 ARG cc_start: 0.8976 (mmm160) cc_final: 0.8458 (mmm160)
REVERT: D  247 MET cc_start: 0.8746 (ttt) cc_final: 0.8413 (ttt)
REVERT: D  248 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8633 (pp30)
REVERT: D  261 LYS cc_start: 0.8591 (tptp) cc_final: 0.8168 (tptp)
REVERT: D  263 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7993 (pm20)
REVERT: E  240 ASN cc_start: 0.8596 (t0) cc_final: 0.8242 (t0)
  outliers start: 15
  outliers final: 4
  residues processed: 128
  average time/residue: 1.2351
  time to fit residues: 169.0300
Evaluate side-chains
  116 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain E residue  216 ASN
Chi-restraints excluded: chain E residue  275 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.092503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.069065 restraints weight = 20608.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 3.79
r_work: 0.2974 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9192  Z= 0.323
  Angle     :  0.656   9.107  12466  Z= 0.337
  Chirality :  0.044   0.149   1404
  Planarity :  0.004   0.041   1585
  Dihedral  :  4.477  22.492   1259
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.41 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.44 (0.26), residues: 1132
  helix:  1.59 (0.27), residues: 401
  sheet: -0.07 (0.33), residues: 258
  loop : -2.16 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.016   0.002   PHE D 229 
 TYR   0.010   0.001   TYR E 285 
 ARG   0.005   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8198 (m-80) cc_final: 0.7305 (m-80)
REVERT: B  215 GLU cc_start: 0.9052 (mp0) cc_final: 0.8848 (mp0)
REVERT: B  217 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6242 (pp-130)
REVERT: C   46 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9224 (pmtt)
REVERT: C   48 ASP cc_start: 0.8614 (m-30) cc_final: 0.8320 (m-30)
REVERT: D   51 MET cc_start: 0.7546 (mmm) cc_final: 0.7269 (mmm)
REVERT: D   75 ILE cc_start: 0.9020 (mm) cc_final: 0.8817 (mp)
REVERT: D  177 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8792 (tpp-160)
REVERT: D  247 MET cc_start: 0.8918 (ttt) cc_final: 0.8515 (ttt)
REVERT: D  251 GLU cc_start: 0.9161 (pt0) cc_final: 0.8801 (pm20)
REVERT: D  261 LYS cc_start: 0.8647 (tptp) cc_final: 0.8327 (tppp)
REVERT: D  263 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8023 (pm20)
REVERT: E  240 ASN cc_start: 0.8562 (t0) cc_final: 0.8291 (t0)
REVERT: E  310 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7835 (mm)
REVERT: E  350 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7614 (m-80)
  outliers start: 21
  outliers final: 8
  residues processed: 125
  average time/residue: 1.2199
  time to fit residues: 163.1330
Evaluate side-chains
  111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Chi-restraints excluded: chain E residue  350 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 67 optimal weight:    0.5980
   chunk 97 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.094800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.071347 restraints weight = 20519.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 3.81
r_work: 0.3020 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9192  Z= 0.181
  Angle     :  0.633   9.755  12466  Z= 0.317
  Chirality :  0.042   0.155   1404
  Planarity :  0.004   0.042   1585
  Dihedral  :  4.309  21.921   1259
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.37 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.28 (0.26), residues: 1132
  helix:  1.87 (0.27), residues: 394
  sheet: -0.01 (0.34), residues: 253
  loop : -2.13 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.001   PHE E  49 
 TYR   0.023   0.001   TYR E 279 
 ARG   0.006   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9286 (mttm) cc_final: 0.9056 (ptpp)
REVERT: A   79 PHE cc_start: 0.7060 (t80) cc_final: 0.6829 (t80)
REVERT: B   59 TYR cc_start: 0.8086 (m-80) cc_final: 0.7264 (m-80)
REVERT: B  215 GLU cc_start: 0.9046 (mp0) cc_final: 0.8839 (mp0)
REVERT: B  217 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6385 (pp-130)
REVERT: B  262 MET cc_start: 0.8295 (tpp) cc_final: 0.7980 (tpp)
REVERT: C   46 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9210 (pmtt)
REVERT: C   48 ASP cc_start: 0.8490 (m-30) cc_final: 0.8058 (m-30)
REVERT: D   35 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7956 (tpp80)
REVERT: D   51 MET cc_start: 0.7522 (mmm) cc_final: 0.7228 (mmm)
REVERT: D   75 ILE cc_start: 0.9019 (mm) cc_final: 0.8749 (mp)
REVERT: D  177 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8758 (tpp-160)
REVERT: D  237 GLU cc_start: 0.8474 (pm20) cc_final: 0.8140 (pm20)
REVERT: D  247 MET cc_start: 0.8906 (ttt) cc_final: 0.8532 (ttt)
REVERT: D  251 GLU cc_start: 0.9166 (pt0) cc_final: 0.8953 (pm20)
REVERT: D  261 LYS cc_start: 0.8604 (tptp) cc_final: 0.8304 (tppp)
REVERT: D  263 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8072 (pm20)
REVERT: E  240 ASN cc_start: 0.8615 (t0) cc_final: 0.8328 (t0)
REVERT: E  310 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7134 (mm)
REVERT: E  311 ASN cc_start: 0.8549 (m110) cc_final: 0.8077 (p0)
  outliers start: 26
  outliers final: 10
  residues processed: 136
  average time/residue: 1.1974
  time to fit residues: 174.8535
Evaluate side-chains
  119 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 MET
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 186 ASN
D 203 GLN
E 216 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.095120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.071757 restraints weight = 20196.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 3.78
r_work: 0.3031 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9192  Z= 0.177
  Angle     :  0.627   9.932  12466  Z= 0.313
  Chirality :  0.042   0.168   1404
  Planarity :  0.004   0.045   1585
  Dihedral  :  4.234  18.109   1259
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.20 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.28 (0.26), residues: 1132
  helix:  1.87 (0.27), residues: 395
  sheet:  0.09 (0.34), residues: 249
  loop : -2.19 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 295 
 PHE   0.024   0.001   PHE D 229 
 TYR   0.010   0.001   TYR E 285 
 ARG   0.007   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9281 (mttm) cc_final: 0.9057 (ptpp)
REVERT: B  215 GLU cc_start: 0.9050 (mp0) cc_final: 0.8832 (mp0)
REVERT: B  217 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6495 (pp-130)
REVERT: B  262 MET cc_start: 0.8404 (tpp) cc_final: 0.8146 (tpp)
REVERT: C   46 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9208 (pmtt)
REVERT: C   48 ASP cc_start: 0.8435 (m-30) cc_final: 0.8003 (m-30)
REVERT: D   35 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7976 (tpp80)
REVERT: D   51 MET cc_start: 0.7522 (mmm) cc_final: 0.7215 (mmm)
REVERT: D   75 ILE cc_start: 0.9035 (mm) cc_final: 0.8764 (mp)
REVERT: D  110 MET cc_start: 0.7091 (tmm) cc_final: 0.6595 (tmm)
REVERT: D  177 ARG cc_start: 0.9001 (mmm160) cc_final: 0.8739 (tpp-160)
REVERT: D  247 MET cc_start: 0.8882 (ttt) cc_final: 0.8501 (ttt)
REVERT: D  251 GLU cc_start: 0.9162 (pt0) cc_final: 0.8941 (pm20)
REVERT: D  261 LYS cc_start: 0.8616 (tptp) cc_final: 0.8085 (tptp)
REVERT: D  263 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8122 (pm20)
REVERT: E  237 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8129 (p0)
REVERT: E  240 ASN cc_start: 0.8614 (t0) cc_final: 0.8323 (t0)
REVERT: E  310 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7107 (mm)
REVERT: E  311 ASN cc_start: 0.8532 (m110) cc_final: 0.8063 (p0)
  outliers start: 22
  outliers final: 12
  residues processed: 132
  average time/residue: 1.2048
  time to fit residues: 170.7379
Evaluate side-chains
  125 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  221 MET
Chi-restraints excluded: chain E residue  237 ASP
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0570
   overall best weight:    1.3304

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.093916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.070534 restraints weight = 20661.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 3.80
r_work: 0.3004 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9192  Z= 0.232
  Angle     :  0.649  10.949  12466  Z= 0.325
  Chirality :  0.042   0.165   1404
  Planarity :  0.004   0.045   1585
  Dihedral  :  4.281  20.747   1259
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.23 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.31 (0.26), residues: 1132
  helix:  1.80 (0.27), residues: 396
  sheet:  0.07 (0.34), residues: 254
  loop : -2.19 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.023   0.001   PHE D 229 
 TYR   0.025   0.001   TYR E 279 
 ARG   0.005   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9299 (mttm) cc_final: 0.9050 (ptpp)
REVERT: B  217 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6652 (pp-130)
REVERT: B  262 MET cc_start: 0.8485 (tpp) cc_final: 0.8223 (tpp)
REVERT: C   46 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9180 (pmtt)
REVERT: D   51 MET cc_start: 0.7547 (mmm) cc_final: 0.7319 (mmm)
REVERT: D   75 ILE cc_start: 0.9061 (mm) cc_final: 0.8795 (mp)
REVERT: D  104 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7490 (ptp90)
REVERT: D  166 VAL cc_start: 0.9004 (t) cc_final: 0.8699 (t)
REVERT: D  177 ARG cc_start: 0.9002 (mmm160) cc_final: 0.8736 (tpp-160)
REVERT: D  251 GLU cc_start: 0.9171 (pt0) cc_final: 0.8953 (pm20)
REVERT: D  261 LYS cc_start: 0.8668 (tptp) cc_final: 0.8336 (tppp)
REVERT: D  263 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8112 (pm20)
REVERT: E  237 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8150 (p0)
REVERT: E  240 ASN cc_start: 0.8626 (t0) cc_final: 0.8337 (t0)
REVERT: E  310 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7151 (mm)
REVERT: E  311 ASN cc_start: 0.8547 (m110) cc_final: 0.8072 (p0)
  outliers start: 20
  outliers final: 14
  residues processed: 125
  average time/residue: 1.2663
  time to fit residues: 169.7028
Evaluate side-chains
  124 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  237 ASP
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 80 optimal weight:    0.2980
   chunk 97 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.094189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.070722 restraints weight = 20772.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.81
r_work: 0.3009 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9192  Z= 0.228
  Angle     :  0.662  11.306  12466  Z= 0.330
  Chirality :  0.043   0.164   1404
  Planarity :  0.004   0.047   1585
  Dihedral  :  4.287  19.283   1259
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.34 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.26), residues: 1132
  helix:  1.79 (0.27), residues: 396
  sheet:  0.04 (0.33), residues: 254
  loop : -2.21 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.022   0.001   PHE E  49 
 TYR   0.010   0.001   TYR E 285 
 ARG   0.004   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9008 (mt0) cc_final: 0.8624 (mt0)
REVERT: B   59 TYR cc_start: 0.8056 (m-80) cc_final: 0.7703 (m-80)
REVERT: B  217 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6736 (pp-130)
REVERT: B  262 MET cc_start: 0.8500 (tpp) cc_final: 0.8229 (tpp)
REVERT: C   46 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9154 (pmtt)
REVERT: D   51 MET cc_start: 0.7567 (mmm) cc_final: 0.7334 (mmm)
REVERT: D   75 ILE cc_start: 0.9065 (mm) cc_final: 0.8799 (mp)
REVERT: D  104 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7513 (ptp90)
REVERT: D  166 VAL cc_start: 0.9030 (t) cc_final: 0.8722 (t)
REVERT: D  177 ARG cc_start: 0.8991 (mmm160) cc_final: 0.8717 (tpp-160)
REVERT: D  261 LYS cc_start: 0.8685 (tptp) cc_final: 0.8366 (tppp)
REVERT: D  263 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8114 (pm20)
REVERT: E  237 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8158 (p0)
REVERT: E  240 ASN cc_start: 0.8622 (t0) cc_final: 0.8332 (t0)
REVERT: E  310 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7185 (mm)
REVERT: E  311 ASN cc_start: 0.8542 (m110) cc_final: 0.8072 (p0)
REVERT: E  350 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7304 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 133
  average time/residue: 1.1893
  time to fit residues: 169.7764
Evaluate side-chains
  127 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  237 ASP
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Chi-restraints excluded: chain E residue  350 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
D 186 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.094857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.071454 restraints weight = 20498.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 3.80
r_work: 0.3026 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9192  Z= 0.206
  Angle     :  0.665  12.159  12466  Z= 0.336
  Chirality :  0.043   0.175   1404
  Planarity :  0.004   0.046   1585
  Dihedral  :  4.248  20.021   1259
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.16 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.26), residues: 1132
  helix:  1.78 (0.27), residues: 399
  sheet:  0.09 (0.33), residues: 256
  loop : -2.27 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 295 
 PHE   0.018   0.001   PHE D 229 
 TYR   0.026   0.001   TYR E 279 
 ARG   0.004   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6772 (pp-130)
REVERT: B  262 MET cc_start: 0.8560 (tpp) cc_final: 0.8354 (tpp)
REVERT: C   46 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9162 (pmtt)
REVERT: D   51 MET cc_start: 0.7576 (mmm) cc_final: 0.7344 (mmm)
REVERT: D   75 ILE cc_start: 0.9053 (mm) cc_final: 0.8781 (mp)
REVERT: D  104 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7488 (ptp90)
REVERT: D  166 VAL cc_start: 0.9034 (t) cc_final: 0.8727 (t)
REVERT: D  177 ARG cc_start: 0.8972 (mmm160) cc_final: 0.8599 (tpp-160)
REVERT: D  261 LYS cc_start: 0.8671 (tptp) cc_final: 0.8375 (tppp)
REVERT: D  263 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8124 (pm20)
REVERT: E  237 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8193 (p0)
REVERT: E  240 ASN cc_start: 0.8620 (t0) cc_final: 0.8325 (t0)
REVERT: E  310 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7125 (mm)
REVERT: E  311 ASN cc_start: 0.8521 (m110) cc_final: 0.8050 (p0)
REVERT: E  350 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7217 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 1.1998
  time to fit residues: 161.0880
Evaluate side-chains
  125 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  237 ASP
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Chi-restraints excluded: chain E residue  350 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 29 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0870
   chunk 76 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0030
   chunk 34 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7370

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.095391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.071899 restraints weight = 20502.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.81
r_work: 0.3033 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9192  Z= 0.199
  Angle     :  0.670  13.223  12466  Z= 0.336
  Chirality :  0.042   0.171   1404
  Planarity :  0.004   0.046   1585
  Dihedral  :  4.235  19.314   1259
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.37 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.26), residues: 1132
  helix:  1.79 (0.27), residues: 398
  sheet:  0.13 (0.33), residues: 256
  loop : -2.28 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 295 
 PHE   0.017   0.001   PHE D 229 
 TYR   0.010   0.001   TYR E 285 
 ARG   0.004   0.000   ARG D 104 

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  217 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6811 (pp-130)
REVERT: B  262 MET cc_start: 0.8563 (tpp) cc_final: 0.8358 (tpp)
REVERT: C   46 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9165 (pmtt)
REVERT: D   51 MET cc_start: 0.7563 (mmm) cc_final: 0.7333 (mmm)
REVERT: D   75 ILE cc_start: 0.9049 (mm) cc_final: 0.8788 (mp)
REVERT: D  104 ARG cc_start: 0.7954 (ptp90) cc_final: 0.7481 (ptp90)
REVERT: D  166 VAL cc_start: 0.9045 (t) cc_final: 0.8744 (t)
REVERT: D  177 ARG cc_start: 0.9006 (mmm160) cc_final: 0.8615 (tpp-160)
REVERT: D  261 LYS cc_start: 0.8650 (tptp) cc_final: 0.8370 (tppp)
REVERT: D  263 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8144 (pm20)
REVERT: E  237 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8185 (p0)
REVERT: E  240 ASN cc_start: 0.8609 (t0) cc_final: 0.8310 (t0)
REVERT: E  259 GLN cc_start: 0.9116 (tt0) cc_final: 0.8865 (tp40)
REVERT: E  310 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7104 (mm)
REVERT: E  311 ASN cc_start: 0.8501 (m110) cc_final: 0.8040 (p0)
REVERT: E  350 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7286 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 122
  average time/residue: 1.2012
  time to fit residues: 158.2379
Evaluate side-chains
  124 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   62 PHE
Chi-restraints excluded: chain D residue  126 ASP
Chi-restraints excluded: chain D residue  162 SER
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  237 ASP
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  310 LEU
Chi-restraints excluded: chain E residue  350 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0670
   chunk 55 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 49 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.8120

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.095567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.072202 restraints weight = 20334.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 3.77
r_work: 0.3039 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9192  Z= 0.200
  Angle     :  0.670  13.884  12466  Z= 0.337
  Chirality :  0.043   0.178   1404
  Planarity :  0.004   0.046   1585
  Dihedral  :  4.212  19.587   1259
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 23.68 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.18 %
    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: -0.30 (0.26), residues: 1132
  helix:  1.78 (0.27), residues: 398
  sheet:  0.20 (0.33), residues: 256
  loop : -2.27 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 295 
 PHE   0.017   0.001   PHE D 229 
 TYR   0.026   0.001   TYR E 279 
 ARG   0.004   0.000   ARG D 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6986.13 seconds
wall clock time: 124 minutes 10.47 seconds (7450.47 seconds total)