Starting phenix.real_space_refine
on Wed Apr 30 02:01:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xgs_38331/04_2025/8xgs_38331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xgs_38331/04_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_38331/04_2025/8xgs_38331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xgs_38331/04_2025/8xgs_38331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xgs_38331/04_2025/8xgs_38331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xgs_38331/04_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-5669/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: 5.43, per 1000 atoms: 0.60
  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: 2.50
  Conformation dependent library (CDL) restraints added in 993.5 milliseconds
  

  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: 1.21
  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: 2.14

  Time building geometry restraints manager: 2.89 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.050
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.070
  Find NCS groups from input model:        0.130
  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:12.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.170
-------------------------------------------------------------------------------
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   9195  Z= 0.392
  Angle     :  0.607   9.601  12470  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17989 (  388)
  hydrogen bonds       : angle       6.39294 ( 1092)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       0.53876 (    4)
  covalent geometry    : bond        0.00582 ( 9192)
  covalent geometry    : angle       0.60702 (12466)
  Misc. bond           : bond        0.01664 (    1)

*********************** 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  : 1.087 
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: 1.1323
  time to fit residues: 194.3349
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  : 1.069 
-------------------------------------------------------------------------------
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 = 0.097029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073917 restraints weight = 20039.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.77
r_work: 0.3077 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
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   9195  Z= 0.122
  Angle     :  0.642  10.700  12470  Z= 0.324
  Chirality :  0.049   0.933   1404
  Planarity :  0.004   0.036   1585
  Dihedral  :  4.452  34.694   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04175 (  388)
  hydrogen bonds       : angle       4.77449 ( 1092)
  SS BOND              : bond        0.00318 (    2)
  SS BOND              : angle       0.88535 (    4)
  covalent geometry    : bond        0.00259 ( 9192)
  covalent geometry    : angle       0.64198 (12466)
  Misc. bond           : bond        0.00022 (    1)

*********************** 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  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9010 (ptpp)
REVERT: B  262 MET cc_start: 0.8364 (tpp) cc_final: 0.8132 (tpp)
REVERT: C   48 ASP cc_start: 0.8400 (m-30) cc_final: 0.8101 (m-30)
REVERT: D   51 MET cc_start: 0.7597 (mmm) cc_final: 0.7350 (mmm)
REVERT: D   60 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8940 (mppt)
REVERT: D  110 MET cc_start: 0.6601 (tmm) cc_final: 0.6253 (tmm)
REVERT: D  177 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8789 (tpp-160)
REVERT: D  251 GLU cc_start: 0.9163 (pt0) cc_final: 0.8830 (pm20)
REVERT: D  261 LYS cc_start: 0.8602 (tptp) cc_final: 0.8082 (tptp)
REVERT: D  263 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7965 (pm20)
REVERT: E  285 TYR cc_start: 0.8474 (m-80) cc_final: 0.8274 (m-80)
REVERT: E  350 TYR cc_start: 0.8338 (m-80) cc_final: 0.7569 (m-80)
  outliers start: 15
  outliers final: 5
  residues processed: 137
  average time/residue: 1.1904
  time to fit residues: 175.1291
Evaluate side-chains
  118 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3641 r_free = 0.3641 target = 0.097175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.074035 restraints weight = 20252.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.78
r_work: 0.3076 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9195  Z= 0.116
  Angle     :  0.610   7.881  12470  Z= 0.309
  Chirality :  0.043   0.415   1404
  Planarity :  0.004   0.037   1585
  Dihedral  :  4.224  23.459   1259
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.62 %
    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:  0.05 (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   0.024   0.001   PHE D  85 
 TYR   0.019   0.001   TYR E 279 
 ARG   0.002   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  388)
  hydrogen bonds       : angle       4.45897 ( 1092)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.74087 (    4)
  covalent geometry    : bond        0.00247 ( 9192)
  covalent geometry    : angle       0.60985 (12466)
  Misc. bond           : bond        0.00026 (    1)

*********************** 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: 13
    poor density    : 125
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  215 GLU cc_start: 0.9033 (mp0) cc_final: 0.8697 (pm20)
REVERT: B  217 MET cc_start: 0.6833 (ptm) cc_final: 0.5986 (pp-130)
REVERT: B  262 MET cc_start: 0.8475 (tpp) cc_final: 0.8216 (tpp)
REVERT: C   46 LYS cc_start: 0.9551 (pmmt) cc_final: 0.9204 (pmtt)
REVERT: C   48 ASP cc_start: 0.8381 (m-30) cc_final: 0.8079 (m-30)
REVERT: D   51 MET cc_start: 0.7607 (mmm) cc_final: 0.7340 (mmm)
REVERT: D   75 ILE cc_start: 0.8974 (mm) cc_final: 0.8756 (mp)
REVERT: D  110 MET cc_start: 0.6837 (tmm) cc_final: 0.6338 (tmm)
REVERT: D  177 ARG cc_start: 0.8975 (mmm160) cc_final: 0.8455 (mmm160)
REVERT: D  237 GLU cc_start: 0.8449 (pm20) cc_final: 0.8122 (pm20)
REVERT: D  247 MET cc_start: 0.8758 (ttt) cc_final: 0.8442 (ttt)
REVERT: D  248 GLN cc_start: 0.9262 (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: 0.8532 (tm-30) cc_final: 0.7992 (pm20)
REVERT: E  240 ASN cc_start: 0.8595 (t0) cc_final: 0.8227 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 130
  average time/residue: 1.2204
  time to fit residues: 170.1063
Evaluate side-chains
  114 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.094077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.070748 restraints weight = 20457.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 3.78
r_work: 0.3008 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9195  Z= 0.168
  Angle     :  0.624   8.773  12470  Z= 0.319
  Chirality :  0.042   0.155   1404
  Planarity :  0.004   0.040   1585
  Dihedral  :  4.329  21.797   1259
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.89 %
    Favored  : 79.94 %
  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: -0.35 (0.26), residues: 1132
  helix:  1.73 (0.27), residues: 400
  sheet: -0.02 (0.34), residues: 253
  loop : -2.16 (0.27), residues: 479

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   0.015   0.001   PHE D 229 
 TYR   0.011   0.001   TYR E 285 
 ARG   0.005   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04305 (  388)
  hydrogen bonds       : angle       4.43376 ( 1092)
  SS BOND              : bond        0.00354 (    2)
  SS BOND              : angle       1.02144 (    4)
  covalent geometry    : bond        0.00388 ( 9192)
  covalent geometry    : angle       0.62353 (12466)
  Misc. bond           : bond        0.00059 (    1)

*********************** 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
  133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9067 (ptpp)
REVERT: C   46 LYS cc_start: 0.9582 (OUTLIER) cc_final: 0.9237 (pmtt)
REVERT: C   48 ASP cc_start: 0.8508 (m-30) cc_final: 0.8190 (m-30)
REVERT: D   51 MET cc_start: 0.7539 (mmm) cc_final: 0.7264 (mmm)
REVERT: D   75 ILE cc_start: 0.8993 (mm) cc_final: 0.8755 (mp)
REVERT: D  110 MET cc_start: 0.6897 (tmm) cc_final: 0.6439 (tmm)
REVERT: D  177 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8778 (tpp-160)
REVERT: D  247 MET cc_start: 0.8987 (ttt) cc_final: 0.8736 (ttt)
REVERT: D  248 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8706 (pp30)
REVERT: D  251 GLU cc_start: 0.9158 (pt0) cc_final: 0.8499 (pp20)
REVERT: D  261 LYS cc_start: 0.8586 (tptp) cc_final: 0.8305 (tppp)
REVERT: D  263 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8020 (pm20)
REVERT: E  240 ASN cc_start: 0.8597 (t0) cc_final: 0.8283 (t0)
REVERT: E  278 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8214 (mpp)
REVERT: E  310 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7755 (mm)
  outliers start: 21
  outliers final: 8
  residues processed: 124
  average time/residue: 1.3378
  time to fit residues: 177.6060
Evaluate side-chains
  110 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  306 THR
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 D residue  248 GLN
Chi-restraints excluded: chain E residue  212 HIS
Chi-restraints excluded: chain E residue  275 GLU
Chi-restraints excluded: chain E residue  278 MET
Chi-restraints excluded: chain E residue  310 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
D 203 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 = 0.3612 r_free = 0.3612 target = 0.095354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071908 restraints weight = 20557.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.82
r_work: 0.3031 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9195  Z= 0.127
  Angle     :  0.627   9.773  12470  Z= 0.314
  Chirality :  0.042   0.161   1404
  Planarity :  0.004   0.041   1585
  Dihedral  :  4.246  22.124   1259
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.65 %
    Favored  : 77.97 %
  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: -0.26 (0.26), residues: 1132
  helix:  1.91 (0.27), residues: 393
  sheet:  0.04 (0.34), residues: 253
  loop : -2.15 (0.27), residues: 486

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   0.014   0.001   PHE E  49 
 TYR   0.024   0.001   TYR E 279 
 ARG   0.007   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  388)
  hydrogen bonds       : angle       4.32926 ( 1092)
  SS BOND              : bond        0.00393 (    2)
  SS BOND              : angle       0.81687 (    4)
  covalent geometry    : bond        0.00285 ( 9192)
  covalent geometry    : angle       0.62647 (12466)
  Misc. bond           : bond        0.00035 (    1)

*********************** 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
  142 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9302 (mttm) cc_final: 0.9070 (ptpp)
REVERT: B  215 GLU cc_start: 0.8918 (mp0) cc_final: 0.8705 (pm20)
REVERT: B  217 MET cc_start: 0.6973 (ptt) cc_final: 0.6423 (pp-130)
REVERT: B  262 MET cc_start: 0.8311 (tpp) cc_final: 0.8003 (tpp)
REVERT: C   46 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9214 (pmtt)
REVERT: C   48 ASP cc_start: 0.8412 (m-30) cc_final: 0.7998 (m-30)
REVERT: D   35 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7944 (tpp80)
REVERT: D   51 MET cc_start: 0.7523 (mmm) cc_final: 0.7234 (mmm)
REVERT: D   75 ILE cc_start: 0.9021 (mm) cc_final: 0.8752 (mp)
REVERT: D  110 MET cc_start: 0.6934 (tmm) cc_final: 0.6465 (tmm)
REVERT: D  177 ARG cc_start: 0.9009 (mmm160) cc_final: 0.8758 (tpp-160)
REVERT: D  247 MET cc_start: 0.8936 (ttt) cc_final: 0.8690 (ttt)
REVERT: D  251 GLU cc_start: 0.9156 (pt0) cc_final: 0.8878 (pm20)
REVERT: D  261 LYS cc_start: 0.8575 (tptp) cc_final: 0.8047 (tptp)
REVERT: D  263 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8074 (pm20)
REVERT: E  240 ASN cc_start: 0.8637 (t0) cc_final: 0.8304 (t0)
REVERT: E  310 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7784 (mm)
  outliers start: 23
  outliers final: 11
  residues processed: 134
  average time/residue: 1.2341
  time to fit residues: 177.1749
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  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  306 THR
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 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:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0370
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
E 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.096215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.073029 restraints weight = 20076.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.76
r_work: 0.3058 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9195  Z= 0.115
  Angle     :  0.620   9.432  12470  Z= 0.310
  Chirality :  0.041   0.165   1404
  Planarity :  0.004   0.044   1585
  Dihedral  :  4.155  18.203   1259
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.20 %
    Favored  : 76.73 %
  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: -0.23 (0.26), residues: 1132
  helix:  1.94 (0.27), residues: 394
  sheet:  0.19 (0.34), residues: 249
  loop : -2.22 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.024   0.001   PHE D 229 
 TYR   0.011   0.001   TYR E 285 
 ARG   0.008   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  388)
  hydrogen bonds       : angle       4.24742 ( 1092)
  SS BOND              : bond        0.00379 (    2)
  SS BOND              : angle       0.75005 (    4)
  covalent geometry    : bond        0.00250 ( 9192)
  covalent geometry    : angle       0.61991 (12466)
  Misc. bond           : bond        0.00023 (    1)

*********************** 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
  135 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9299 (mttm) cc_final: 0.9061 (ptpp)
REVERT: A   79 PHE cc_start: 0.6971 (t80) cc_final: 0.6767 (t80)
REVERT: B   66 ASP cc_start: 0.8952 (p0) cc_final: 0.8750 (p0)
REVERT: B  215 GLU cc_start: 0.8970 (mp0) cc_final: 0.8625 (pm20)
REVERT: B  217 MET cc_start: 0.6943 (ptt) cc_final: 0.6399 (pp-130)
REVERT: B  262 MET cc_start: 0.8393 (tpp) cc_final: 0.8134 (tpp)
REVERT: C   46 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9210 (pmtt)
REVERT: C   48 ASP cc_start: 0.8339 (m-30) cc_final: 0.7995 (m-30)
REVERT: D   51 MET cc_start: 0.7532 (mmm) cc_final: 0.7232 (mmm)
REVERT: D   75 ILE cc_start: 0.9018 (mm) cc_final: 0.8764 (mp)
REVERT: D  110 MET cc_start: 0.6965 (tmm) cc_final: 0.6439 (tmm)
REVERT: D  166 VAL cc_start: 0.9058 (t) cc_final: 0.8765 (t)
REVERT: D  177 ARG cc_start: 0.9007 (mmm160) cc_final: 0.8748 (tpp-160)
REVERT: D  247 MET cc_start: 0.8745 (ttt) cc_final: 0.8481 (ttt)
REVERT: D  251 GLU cc_start: 0.9150 (pt0) cc_final: 0.8485 (pp20)
REVERT: D  261 LYS cc_start: 0.8591 (tptp) cc_final: 0.8012 (tptp)
REVERT: D  263 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8102 (pm20)
REVERT: E  240 ASN cc_start: 0.8635 (t0) cc_final: 0.8290 (t0)
REVERT: E  310 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7741 (mm)
  outliers start: 20
  outliers final: 10
  residues processed: 126
  average time/residue: 1.2349
  time to fit residues: 167.1204
Evaluate side-chains
  118 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  306 THR
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  164 VAL
Chi-restraints excluded: chain E residue   29 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 90 optimal weight:    0.2980
   chunk 15 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 108 optimal weight:    0.1980
   chunk 47 optimal weight:    0.3980
   chunk 89 optimal weight:    0.1980
   chunk 52 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0020
   overall best weight:    0.2188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.097223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.074036 restraints weight = 20327.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.79
r_work: 0.3082 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9195  Z= 0.113
  Angle     :  0.621   9.730  12470  Z= 0.310
  Chirality :  0.041   0.166   1404
  Planarity :  0.004   0.043   1585
  Dihedral  :  4.081  20.626   1259
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 22.44 %
    Favored  : 76.01 %
  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: -0.17 (0.26), residues: 1132
  helix:  1.98 (0.28), residues: 394
  sheet:  0.30 (0.35), residues: 249
  loop : -2.23 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.000   HIS B  54 
 PHE   0.018   0.001   PHE D 229 
 TYR   0.025   0.001   TYR E 279 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  388)
  hydrogen bonds       : angle       4.17203 ( 1092)
  SS BOND              : bond        0.00376 (    2)
  SS BOND              : angle       0.61028 (    4)
  covalent geometry    : bond        0.00244 ( 9192)
  covalent geometry    : angle       0.62134 (12466)
  Misc. bond           : bond        0.00010 (    1)

*********************** 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
  137 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9293 (mttm) cc_final: 0.9057 (ptpp)
REVERT: B   66 ASP cc_start: 0.8945 (p0) cc_final: 0.8704 (p0)
REVERT: B  215 GLU cc_start: 0.8983 (mp0) cc_final: 0.8565 (pm20)
REVERT: B  217 MET cc_start: 0.6856 (ptt) cc_final: 0.6311 (pp-130)
REVERT: B  262 MET cc_start: 0.8429 (tpp) cc_final: 0.8123 (tpp)
REVERT: C   46 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9194 (pmtt)
REVERT: C   48 ASP cc_start: 0.8221 (m-30) cc_final: 0.7865 (m-30)
REVERT: D   51 MET cc_start: 0.7590 (mmm) cc_final: 0.7292 (mmm)
REVERT: D  104 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7450 (ptp90)
REVERT: D  110 MET cc_start: 0.6839 (tmm) cc_final: 0.6341 (tmm)
REVERT: D  177 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8706 (tpp-160)
REVERT: D  247 MET cc_start: 0.8699 (ttt) cc_final: 0.8447 (ttt)
REVERT: D  251 GLU cc_start: 0.9155 (pt0) cc_final: 0.8493 (pp20)
REVERT: D  261 LYS cc_start: 0.8590 (tptp) cc_final: 0.8077 (tptp)
REVERT: D  263 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8138 (pm20)
REVERT: E  237 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8117 (p0)
REVERT: E  240 ASN cc_start: 0.8642 (t0) cc_final: 0.8277 (t0)
REVERT: E  310 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (mm)
REVERT: E  327 ASP cc_start: 0.8521 (t0) cc_final: 0.8072 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 1.2917
  time to fit residues: 184.8827
Evaluate side-chains
  126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
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  226 GLU
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 D residue  126 ASP
Chi-restraints excluded: chain D residue  164 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 103 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 110 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3628 r_free = 0.3628 target = 0.096458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.073137 restraints weight = 20638.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.81
r_work: 0.3058 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9195  Z= 0.129
  Angle     :  0.642  10.398  12470  Z= 0.321
  Chirality :  0.042   0.168   1404
  Planarity :  0.004   0.045   1585
  Dihedral  :  4.098  19.274   1259
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.23 %
    Favored  : 75.80 %
  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: -0.20 (0.26), residues: 1132
  helix:  1.94 (0.27), residues: 394
  sheet:  0.26 (0.34), residues: 249
  loop : -2.22 (0.26), residues: 489

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   0.019   0.001   PHE D 229 
 TYR   0.009   0.001   TYR E 285 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  388)
  hydrogen bonds       : angle       4.18582 ( 1092)
  SS BOND              : bond        0.00420 (    2)
  SS BOND              : angle       0.73970 (    4)
  covalent geometry    : bond        0.00292 ( 9192)
  covalent geometry    : angle       0.64204 (12466)
  Misc. bond           : bond        0.00032 (    1)

*********************** 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
  131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9303 (mttm) cc_final: 0.9060 (ptpp)
REVERT: B   61 MET cc_start: 0.8301 (pp-130) cc_final: 0.8096 (pp-130)
REVERT: B   66 ASP cc_start: 0.8961 (p0) cc_final: 0.8709 (p0)
REVERT: B  217 MET cc_start: 0.6900 (ptt) cc_final: 0.6281 (pp-130)
REVERT: B  262 MET cc_start: 0.8454 (tpp) cc_final: 0.8155 (tpp)
REVERT: C   46 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9205 (pmtt)
REVERT: C   48 ASP cc_start: 0.8288 (m-30) cc_final: 0.7958 (m-30)
REVERT: D   51 MET cc_start: 0.7618 (mmm) cc_final: 0.7319 (mmm)
REVERT: D   75 ILE cc_start: 0.8929 (mm) cc_final: 0.8712 (mp)
REVERT: D  104 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7441 (ptp90)
REVERT: D  110 MET cc_start: 0.6828 (tmm) cc_final: 0.6303 (tmm)
REVERT: D  166 VAL cc_start: 0.9031 (t) cc_final: 0.8739 (t)
REVERT: D  177 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8712 (tpp-160)
REVERT: D  248 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8589 (pp30)
REVERT: D  251 GLU cc_start: 0.9156 (pt0) cc_final: 0.8483 (pp20)
REVERT: D  261 LYS cc_start: 0.8598 (tptp) cc_final: 0.8320 (tppp)
REVERT: D  263 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8103 (pm20)
REVERT: E  237 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8109 (p0)
REVERT: E  240 ASN cc_start: 0.8647 (t0) cc_final: 0.8318 (t0)
REVERT: E  310 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7737 (mm)
REVERT: E  327 ASP cc_start: 0.8531 (t0) cc_final: 0.8084 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 126
  average time/residue: 1.2220
  time to fit residues: 165.2648
Evaluate side-chains
  121 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
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  226 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 D residue  248 GLN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.0970
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 26 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 110 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3640 r_free = 0.3640 target = 0.096760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.073223 restraints weight = 20436.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 3.82
r_work: 0.3067 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9195  Z= 0.126
  Angle     :  0.671  13.036  12470  Z= 0.333
  Chirality :  0.042   0.172   1404
  Planarity :  0.004   0.044   1585
  Dihedral  :  4.087  20.068   1259
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 23.37 %
    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: -0.26 (0.26), residues: 1132
  helix:  1.85 (0.27), residues: 399
  sheet:  0.26 (0.34), residues: 249
  loop : -2.28 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.017   0.001   PHE D 229 
 TYR   0.025   0.001   TYR E 279 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  388)
  hydrogen bonds       : angle       4.18529 ( 1092)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.67895 (    4)
  covalent geometry    : bond        0.00288 ( 9192)
  covalent geometry    : angle       0.67127 (12466)
  Misc. bond           : bond        0.00025 (    1)

*********************** 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
  126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9302 (mttm) cc_final: 0.9056 (ptpp)
REVERT: B   61 MET cc_start: 0.8341 (pp-130) cc_final: 0.8118 (pp-130)
REVERT: B   66 ASP cc_start: 0.8954 (p0) cc_final: 0.8696 (p0)
REVERT: B  215 GLU cc_start: 0.8878 (mp0) cc_final: 0.8642 (pm20)
REVERT: B  217 MET cc_start: 0.6882 (ptt) cc_final: 0.6338 (pp-130)
REVERT: B  262 MET cc_start: 0.8468 (tpp) cc_final: 0.8221 (tpp)
REVERT: C   46 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9190 (pmtt)
REVERT: C   48 ASP cc_start: 0.8210 (m-30) cc_final: 0.7923 (m-30)
REVERT: D   51 MET cc_start: 0.7608 (mmm) cc_final: 0.7310 (mmm)
REVERT: D  104 ARG cc_start: 0.7813 (ptp90) cc_final: 0.7372 (ptp90)
REVERT: D  110 MET cc_start: 0.6835 (tmm) cc_final: 0.6387 (tmm)
REVERT: D  166 VAL cc_start: 0.9026 (t) cc_final: 0.8734 (t)
REVERT: D  177 ARG cc_start: 0.8990 (mmm160) cc_final: 0.8706 (tpp-160)
REVERT: D  248 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8565 (pp30)
REVERT: D  251 GLU cc_start: 0.9161 (pt0) cc_final: 0.8482 (pp20)
REVERT: D  261 LYS cc_start: 0.8598 (tptp) cc_final: 0.8317 (tppp)
REVERT: D  263 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8142 (pm20)
REVERT: E  237 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8108 (p0)
REVERT: E  240 ASN cc_start: 0.8643 (t0) cc_final: 0.8312 (t0)
REVERT: E  310 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: E  327 ASP cc_start: 0.8533 (t0) cc_final: 0.8139 (t70)
  outliers start: 14
  outliers final: 7
  residues processed: 122
  average time/residue: 1.3246
  time to fit residues: 173.0430
Evaluate side-chains
  119 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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 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  164 VAL
Chi-restraints excluded: chain D residue  248 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 ** 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 = 0.3617 r_free = 0.3617 target = 0.095678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.072180 restraints weight = 20596.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.80
r_work: 0.3041 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9195  Z= 0.149
  Angle     :  0.698  13.959  12470  Z= 0.347
  Chirality :  0.043   0.170   1404
  Planarity :  0.004   0.044   1585
  Dihedral  :  4.161  19.321   1259
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 22.96 %
    Favored  : 75.28 %
  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: -0.27 (0.26), residues: 1132
  helix:  1.78 (0.27), residues: 400
  sheet:  0.21 (0.34), residues: 253
  loop : -2.22 (0.26), residues: 479

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   0.020   0.001   PHE D 229 
 TYR   0.009   0.001   TYR E 285 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  388)
  hydrogen bonds       : angle       4.28674 ( 1092)
  SS BOND              : bond        0.00370 (    2)
  SS BOND              : angle       0.82874 (    4)
  covalent geometry    : bond        0.00351 ( 9192)
  covalent geometry    : angle       0.69783 (12466)
  Misc. bond           : bond        0.00038 (    1)

********************** 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
  125 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 LYS cc_start: 0.9310 (mttm) cc_final: 0.9059 (ptpp)
REVERT: B   59 TYR cc_start: 0.7987 (m-80) cc_final: 0.7447 (m-80)
REVERT: B   66 ASP cc_start: 0.8993 (p0) cc_final: 0.8750 (p0)
REVERT: B  217 MET cc_start: 0.6892 (ptt) cc_final: 0.6240 (pp-130)
REVERT: C   46 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9177 (pmtt)
REVERT: C   48 ASP cc_start: 0.8263 (m-30) cc_final: 0.7963 (m-30)
REVERT: D   51 MET cc_start: 0.7600 (mmm) cc_final: 0.7296 (mmm)
REVERT: D   75 ILE cc_start: 0.8904 (mm) cc_final: 0.8699 (mp)
REVERT: D  104 ARG cc_start: 0.7901 (ptp90) cc_final: 0.7442 (ptp90)
REVERT: D  110 MET cc_start: 0.6954 (tmm) cc_final: 0.6514 (tmm)
REVERT: D  166 VAL cc_start: 0.9024 (t) cc_final: 0.8733 (t)
REVERT: D  177 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8722 (tpp-160)
REVERT: D  261 LYS cc_start: 0.8636 (tptp) cc_final: 0.8333 (tppp)
REVERT: D  263 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8133 (pm20)
REVERT: E  237 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8186 (p0)
REVERT: E  240 ASN cc_start: 0.8638 (t0) cc_final: 0.8315 (t0)
REVERT: E  310 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7796 (mm)
REVERT: E  327 ASP cc_start: 0.8559 (t0) cc_final: 0.8178 (t70)
REVERT: E  350 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7420 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 1.4761
  time to fit residues: 187.9812
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  : 1.102 
-------------------------------------------------------------------------------
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  226 GLU
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  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:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0070
   chunk 49 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
E 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.097176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.073772 restraints weight = 20161.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.76
r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9195  Z= 0.127
  Angle     :  0.694  14.519  12470  Z= 0.342
  Chirality :  0.042   0.171   1404
  Planarity :  0.004   0.044   1585
  Dihedral  :  4.116  19.711   1259
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 23.58 %
    Favored  : 75.28 %
  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: -0.26 (0.26), residues: 1132
  helix:  1.83 (0.27), residues: 398
  sheet:  0.29 (0.34), residues: 249
  loop : -2.27 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.000   HIS B  54 
 PHE   0.017   0.001   PHE D 229 
 TYR   0.026   0.001   TYR E 279 
 ARG   0.004   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  388)
  hydrogen bonds       : angle       4.25378 ( 1092)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       0.73087 (    4)
  covalent geometry    : bond        0.00291 ( 9192)
  covalent geometry    : angle       0.69350 (12466)
  Misc. bond           : bond        0.00023 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7730.35 seconds
wall clock time: 136 minutes 17.13 seconds (8177.13 seconds total)