Starting phenix.real_space_refine
on Mon May 12 12:06:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k7t_36941/05_2025/8k7t_36941.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.124
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      43      5.16       5
     C    5722      2.51       5
     N    1451      2.21       5
     O    1732      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8948
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1743
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208}
    Chain: "G"
      Number of atoms: 297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 297
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "H"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 341
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 1, 'TRANS': 41}
    Chain: "B"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1247
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 1, 'TRANS': 158}
    Chain: "E"
      Number of atoms: 2511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2511
          Classifications: {'peptide': 315}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294}
    Chain: "F"
      Number of atoms: 2511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2511
          Classifications: {'peptide': 315}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "I"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "J"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.28, per 1000 atoms: 0.59
  Number of scatterers: 8948
  At special positions: 0
  Unit cell: (87.15, 102.09, 163.095, 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      43     16.00
     O    1732      8.00
     N    1451      7.00
     C    5722      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  25 " - pdb=" SG  CYS H  25 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 108 " - pdb=" SG  CYS F 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 121 " - pdb=" SG  CYS E 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 196 " - pdb=" SG  CYS F 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 226 " - pdb=" SG  CYS E 285 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 330 " - pdb=" SG  CYS E 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 121 " - pdb=" SG  CYS F 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 226 " - pdb=" SG  CYS F 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 330 " - pdb=" SG  CYS F 392 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA I   3 " - " MAN I   4 "
      " BMA J   3 " - " MAN J   4 "
    ALPHA1-6
      " BMA I   3 " - " MAN I   5 "
      " BMA J   3 " - " MAN J   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
    NAG-ASN
      " NAG A 301 " - " ASN A  73 "
      " NAG A 302 " - " ASN A 167 "
      " NAG A 303 " - " ASN A 152 "
      " NAG C   1 " - " ASN A  66 "
      " NAG D   1 " - " ASN A 106 "
      " NAG E 501 " - " ASN E 238 "
      " NAG E 502 " - " ASN E 166 "
      " NAG F 501 " - " ASN F 166 "
      " NAG F 502 " - " ASN F 238 "
      " NAG I   1 " - " ASN E 261 "
      " NAG J   1 " - " ASN F 261 "
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 937.9 milliseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 19 sheets defined
      28.9% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.834A  pdb=" N   LEU A  55 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLN A  56 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 56'
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 200 through 205
      removed outlier: 3.539A  pdb=" N   GLN A 204 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 236
    Processing helix  chain 'G' and resid 23 through 58
    Processing helix  chain 'H' and resid 21 through 62
      removed outlier: 3.947A  pdb=" N   CYS H  25 " --> pdb=" O   GLU H  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 75
      removed outlier: 5.183A  pdb=" N   LYS B  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   LYS B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   GLU B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 112
      removed outlier: 3.680A  pdb=" N   ARG B 112 " --> pdb=" O   ILE B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 154
      removed outlier: 4.041A  pdb=" N   GLY B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 199
    Processing helix  chain 'E' and resid 168 through 174
      removed outlier: 3.588A  pdb=" N   SER E 174 " --> pdb=" O   GLN E 170 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 212 through 218
    Processing helix  chain 'E' and resid 273 through 280
      removed outlier: 3.858A  pdb=" N   TRP E 277 " --> pdb=" O   VAL E 273 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE E 278 " --> pdb=" O   ALA E 274 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 174
    Processing helix  chain 'F' and resid 212 through 218
    Processing helix  chain 'F' and resid 273 through 280
      removed outlier: 3.942A  pdb=" N   TRP F 277 " --> pdb=" O   VAL F 273 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 381 through 386
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.839A  pdb=" N   ILE A  39 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121
      removed outlier: 4.507A  pdb=" N   TYR A 177 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   LYS A 141 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A 142 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   TYR A 153 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   TYR A 144 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.682A  pdb=" N   GLY A 125 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   PHE A 127 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ARG A 162 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 100 through 105
      removed outlier: 4.743A  pdb=" N   ALA E 159 " --> pdb=" O   GLY E 125 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU E 158 " --> pdb=" O   GLU E 154 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLU E 154 " --> pdb=" O   LEU E 158 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   SER E 160 " --> pdb=" O   ILE E 152 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL E 150 " --> pdb=" O   CYS E 162 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS E 164 " --> pdb=" O   GLN E 148 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLN E 148 " --> pdb=" O   LYS E 164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AA9, first strand: chain 'E' and resid 208 through 209
      removed outlier: 3.756A  pdb=" N   THR E 225 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ASP E 230 " --> pdb=" O   THR E 264 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   THR E 264 " --> pdb=" O   ASP E 230 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 238 through 243
    Processing sheet with id=AB2, first strand: chain 'E' and resid 311 through 315
      removed outlier: 4.257A  pdb=" N   THR E 329 " --> pdb=" O   PHE E 315 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   PHE E 371 " --> pdb=" O   ASN E 334 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 311 through 315
      removed outlier: 4.257A  pdb=" N   THR E 329 " --> pdb=" O   PHE E 315 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   PHE E 371 " --> pdb=" O   ASN E 334 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU E 362 " --> pdb=" O   PHE E 372 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 341 through 344
      removed outlier: 3.820A  pdb=" N   LYS E 407 " --> pdb=" O   CYS E 392 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 100 through 105
    Processing sheet with id=AB6, first strand: chain 'F' and resid 134 through 136
    Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 209
      removed outlier: 3.656A  pdb=" N   ILE F 205 " --> pdb=" O   VAL F 229 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASP F 230 " --> pdb=" O   THR F 264 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   THR F 264 " --> pdb=" O   ASP F 230 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 238 through 243
    Processing sheet with id=AB9, first strand: chain 'F' and resid 311 through 315
      removed outlier: 4.287A  pdb=" N   THR F 329 " --> pdb=" O   PHE F 315 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 349 through 350

    439 hydrogen bonds defined for protein.
    1197 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: 2.64

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1412
        1.30 -     1.43: 2385
        1.43 -     1.56: 5297
        1.56 -     1.69: 2
        1.69 -     1.82: 53
  Bond restraints: 9149
  Sorted by residual:
  bond pdb=" C   PHE A 207 "
       pdb=" O   PHE A 207 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.28e-02 6.10e+03 2.59e+01
  bond pdb=" C   ILE A 206 "
       pdb=" O   ILE A 206 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.052 1.17e-02 7.31e+03 1.95e+01
  bond pdb=" C   ILE A 213 "
       pdb=" O   ILE A 213 "
    ideal  model  delta    sigma   weight residual
    1.237  1.188  0.049 1.13e-02 7.83e+03 1.88e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.491 -0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" C   VAL A 211 "
       pdb=" O   VAL A 211 "
    ideal  model  delta    sigma   weight residual
    1.237  1.189  0.048 1.17e-02 7.31e+03 1.68e+01
  ... (remaining 9144 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 12279
        3.24 -     6.47: 141
        6.47 -     9.71: 17
        9.71 -    12.94: 3
       12.94 -    16.18: 3
  Bond angle restraints: 12443
  Sorted by residual:
  angle pdb=" CB  GLU B 171 "
        pdb=" CG  GLU B 171 "
        pdb=" CD  GLU B 171 "
      ideal   model   delta    sigma   weight residual
     112.60   96.42   16.18 1.70e+00 3.46e-01 9.06e+01
  angle pdb=" C   ILE A 213 "
        pdb=" CA  ILE A 213 "
        pdb=" CB  ILE A 213 "
      ideal   model   delta    sigma   weight residual
     111.97  102.70    9.27 1.28e+00 6.10e-01 5.24e+01
  angle pdb=" N   LEU A 205 "
        pdb=" CA  LEU A 205 "
        pdb=" C   LEU A 205 "
      ideal   model   delta    sigma   weight residual
     113.18  105.05    8.13 1.21e+00 6.83e-01 4.52e+01
  angle pdb=" N   GLU B 171 "
        pdb=" CA  GLU B 171 "
        pdb=" C   GLU B 171 "
      ideal   model   delta    sigma   weight residual
     111.03  103.75    7.28 1.11e+00 8.12e-01 4.30e+01
  angle pdb=" C   ARG A 179 "
        pdb=" CA  ARG A 179 "
        pdb=" CB  ARG A 179 "
      ideal   model   delta    sigma   weight residual
     110.42  123.45  -13.03 1.99e+00 2.53e-01 4.29e+01
  ... (remaining 12438 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.44: 5298
       24.44 -    48.89: 384
       48.89 -    73.33: 51
       73.33 -    97.78: 34
       97.78 -   122.22: 22
  Dihedral angle restraints: 5789
    sinusoidal: 2598
      harmonic: 3191
  Sorted by residual:
  dihedral pdb=" CB  CYS G  25 "
           pdb=" SG  CYS G  25 "
           pdb=" SG  CYS H  25 "
           pdb=" CB  CYS H  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.19   89.19     1      1.00e+01 1.00e-02 9.46e+01
  dihedral pdb=" N   GLU B 171 "
           pdb=" C   GLU B 171 "
           pdb=" CA  GLU B 171 "
           pdb=" CB  GLU B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.21   15.59     0      2.50e+00 1.60e-01 3.89e+01
  dihedral pdb=" C   GLU B 171 "
           pdb=" N   GLU B 171 "
           pdb=" CA  GLU B 171 "
           pdb=" CB  GLU B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.65  -14.95     0      2.50e+00 1.60e-01 3.58e+01
  ... (remaining 5786 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1417
       0.098 -    0.196: 77
       0.196 -    0.293: 10
       0.293 -    0.391: 5
       0.391 -    0.489: 1
  Chirality restraints: 1510
  Sorted by residual:
  chirality pdb=" CA  GLU B 171 "
            pdb=" N   GLU B 171 "
            pdb=" C   GLU B 171 "
            pdb=" CB  GLU B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.00   -0.49 2.00e-01 2.50e+01 5.98e+00
  chirality pdb=" CA  ILE A 213 "
            pdb=" N   ILE A 213 "
            pdb=" C   ILE A 213 "
            pdb=" CB  ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.82   -0.38 2.00e-01 2.50e+01 3.70e+00
  chirality pdb=" C1  NAG E 501 "
            pdb=" ND2 ASN E 238 "
            pdb=" C2  NAG E 501 "
            pdb=" O5  NAG E 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.88e+00
  ... (remaining 1507 not shown)

  Planarity restraints: 1530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 204 "    0.024 2.00e-02 2.50e+03   4.87e-02 2.37e+01
        pdb=" C   GLN A 204 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   GLN A 204 "    0.032 2.00e-02 2.50e+03
        pdb=" N   LEU A 205 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 171 "    0.020 2.00e-02 2.50e+03   4.22e-02 1.78e+01
        pdb=" CD  GLU B 171 "   -0.073 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 171 "    0.027 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 171 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F 200 "    0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   GLU F 200 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLU F 200 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PRO F 201 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1527 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 104
        2.60 -     3.18: 7586
        3.18 -     3.75: 13419
        3.75 -     4.33: 18061
        4.33 -     4.90: 29961
  Nonbonded interactions: 69131
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 203 "
            pdb=" N   ILE A 206 "
     model   vdw
     2.026 3.120
  nonbonded pdb=" OE1 GLN E 118 "
            pdb=" NZ  LYS E 164 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   ASP A 168 "
            pdb=" OH  TYR A 172 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OH  TYR E 120 "
            pdb=" OE2 GLU F 102 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   TYR B 193 "
            pdb=" NE2 GLN B 197 "
     model   vdw
     2.284 3.120
  ... (remaining 69126 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = (chain 'H' and resid 22 through 58)
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.280
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   9184  Z= 0.262
  Angle     :  0.891  16.180  12536  Z= 0.469
  Chirality :  0.053   0.489   1510
  Planarity :  0.005   0.070   1519
  Dihedral  : 18.711 122.219   3683
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.16 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.59 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1072
  helix:  2.02 (0.31), residues: 265
  sheet:  0.26 (0.27), residues: 364
  loop : -1.19 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 172 
 HIS   0.008   0.001   HIS E 105 
 PHE   0.013   0.001   PHE A 207 
 TYR   0.018   0.001   TYR F 313 
 ARG   0.008   0.001   ARG E 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00895 (   11)
  link_NAG-ASN         : angle       4.81424 (   33)
  link_ALPHA1-6        : bond        0.00472 (    2)
  link_ALPHA1-6        : angle       1.51719 (    6)
  link_BETA1-4         : bond        0.00868 (    8)
  link_BETA1-4         : angle       1.82939 (   24)
  link_ALPHA1-3        : bond        0.00426 (    2)
  link_ALPHA1-3        : angle       1.44986 (    6)
  hydrogen bonds       : bond        0.10335 (  420)
  hydrogen bonds       : angle       5.01032 ( 1197)
  SS BOND              : bond        0.00355 (   12)
  SS BOND              : angle       1.07058 (   24)
  covalent geometry    : bond        0.00473 ( 9149)
  covalent geometry    : angle       0.85287 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 252
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   43 TYR cc_start: 0.8488 (t80) cc_final: 0.8124 (t80)
REVERT: H   26 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6471 (m-80)
REVERT: H   28 LEU cc_start: 0.8222 (tt) cc_final: 0.7979 (tt)
REVERT: B  123 LEU cc_start: 0.8378 (tp) cc_final: 0.7901 (tt)
REVERT: E  135 TRP cc_start: 0.8321 (m100) cc_final: 0.7796 (m-10)
  outliers start: 6
  outliers final: 2
  residues processed: 257
  average time/residue: 0.2103
  time to fit residues: 74.0355
Evaluate side-chains
  193 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 190
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain H residue   26 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
B 126 ASN
** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 284 GLN
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 111 ASN
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 393 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.170458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.140450 restraints weight = 15398.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.143103 restraints weight = 9401.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.145231 restraints weight = 6632.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9184  Z= 0.174
  Angle     :  0.769  10.456  12536  Z= 0.365
  Chirality :  0.047   0.329   1510
  Planarity :  0.004   0.055   1519
  Dihedral  : 14.247 110.799   1631
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  5.22 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.27 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.26), residues: 1072
  helix:  1.68 (0.30), residues: 260
  sheet:  0.23 (0.27), residues: 378
  loop : -1.18 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  42 
 HIS   0.003   0.001   HIS E 396 
 PHE   0.022   0.002   PHE E 335 
 TYR   0.022   0.002   TYR B 193 
 ARG   0.006   0.001   ARG G  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00728 (   11)
  link_NAG-ASN         : angle       4.67283 (   33)
  link_ALPHA1-6        : bond        0.00246 (    2)
  link_ALPHA1-6        : angle       2.49235 (    6)
  link_BETA1-4         : bond        0.00420 (    8)
  link_BETA1-4         : angle       2.70908 (   24)
  link_ALPHA1-3        : bond        0.00897 (    2)
  link_ALPHA1-3        : angle       2.14691 (    6)
  hydrogen bonds       : bond        0.03973 (  420)
  hydrogen bonds       : angle       4.49872 ( 1197)
  SS BOND              : bond        0.00963 (   12)
  SS BOND              : angle       1.38328 (   24)
  covalent geometry    : bond        0.00401 ( 9149)
  covalent geometry    : angle       0.71699 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (t)
REVERT: H   26 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6567 (m-80)
REVERT: B   81 ASP cc_start: 0.8767 (p0) cc_final: 0.8224 (p0)
REVERT: B   83 GLU cc_start: 0.7765 (pm20) cc_final: 0.7340 (pm20)
REVERT: B  106 LEU cc_start: 0.9145 (mt) cc_final: 0.8906 (tp)
REVERT: B  171 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7626 (tt0)
  outliers start: 30
  outliers final: 16
  residues processed: 214
  average time/residue: 0.1976
  time to fit residues: 58.7224
Evaluate side-chains
  186 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 THR
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  167 ILE
Chi-restraints excluded: chain E residue  176 SER
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  258 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 59 optimal weight:    0.2980
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 132 HIS
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 118 GLN
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 389 GLN
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 111 ASN
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 199 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.160806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130900 restraints weight = 15716.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131015 restraints weight = 10280.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.132348 restraints weight = 9260.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   9184  Z= 0.241
  Angle     :  0.807   9.901  12536  Z= 0.393
  Chirality :  0.050   0.346   1510
  Planarity :  0.005   0.056   1519
  Dihedral  : 12.763 109.474   1627
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.06 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 18.58 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1072
  helix:  1.50 (0.29), residues: 266
  sheet: -0.03 (0.27), residues: 375
  loop : -1.24 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 277 
 HIS   0.007   0.002   HIS A  65 
 PHE   0.021   0.002   PHE E 335 
 TYR   0.036   0.002   TYR G  43 
 ARG   0.007   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00686 (   11)
  link_NAG-ASN         : angle       4.71532 (   33)
  link_ALPHA1-6        : bond        0.00104 (    2)
  link_ALPHA1-6        : angle       2.89412 (    6)
  link_BETA1-4         : bond        0.00469 (    8)
  link_BETA1-4         : angle       2.60341 (   24)
  link_ALPHA1-3        : bond        0.01026 (    2)
  link_ALPHA1-3        : angle       1.53303 (    6)
  hydrogen bonds       : bond        0.04430 (  420)
  hydrogen bonds       : angle       4.75582 ( 1197)
  SS BOND              : bond        0.00441 (   12)
  SS BOND              : angle       1.61923 (   24)
  covalent geometry    : bond        0.00566 ( 9149)
  covalent geometry    : angle       0.75776 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 179
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8592 (tp) cc_final: 0.8267 (tt)
REVERT: A  128 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8037 (m-30)
REVERT: A  226 GLU cc_start: 0.8293 (pt0) cc_final: 0.7736 (pt0)
REVERT: H   26 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.6153 (m-80)
REVERT: B   81 ASP cc_start: 0.8909 (p0) cc_final: 0.8407 (p0)
REVERT: B   83 GLU cc_start: 0.8015 (pm20) cc_final: 0.7518 (pm20)
REVERT: B   95 TRP cc_start: 0.5506 (t60) cc_final: 0.3981 (t60)
REVERT: B  185 CYS cc_start: 0.7572 (t) cc_final: 0.7244 (t)
REVERT: E  296 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8167 (pt)
REVERT: E  319 GLU cc_start: 0.5718 (tt0) cc_final: 0.5501 (tp30)
REVERT: F  255 TYR cc_start: 0.7588 (p90) cc_final: 0.7201 (p90)
REVERT: F  362 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6807 (mp)
  outliers start: 44
  outliers final: 19
  residues processed: 208
  average time/residue: 0.2124
  time to fit residues: 60.7578
Evaluate side-chains
  183 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   40 THR
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  167 ILE
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  204 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  314 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  362 LEU
Chi-restraints excluded: chain F residue  392 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 13 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    9.9990
   chunk 88 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.163172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131729 restraints weight = 15335.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.134604 restraints weight = 10394.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135822 restraints weight = 7119.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9184  Z= 0.139
  Angle     :  0.728   9.596  12536  Z= 0.351
  Chirality :  0.047   0.352   1510
  Planarity :  0.004   0.059   1519
  Dihedral  : 11.697 106.758   1627
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.50 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.91 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.27), residues: 1072
  helix:  1.69 (0.31), residues: 260
  sheet:  0.05 (0.28), residues: 374
  loop : -1.23 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B  42 
 HIS   0.005   0.001   HIS E 105 
 PHE   0.016   0.001   PHE E 335 
 TYR   0.019   0.001   TYR G  43 
 ARG   0.010   0.001   ARG B  43 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00720 (   11)
  link_NAG-ASN         : angle       4.03489 (   33)
  link_ALPHA1-6        : bond        0.00444 (    2)
  link_ALPHA1-6        : angle       2.35332 (    6)
  link_BETA1-4         : bond        0.00502 (    8)
  link_BETA1-4         : angle       2.51169 (   24)
  link_ALPHA1-3        : bond        0.01132 (    2)
  link_ALPHA1-3        : angle       1.53711 (    6)
  hydrogen bonds       : bond        0.04037 (  420)
  hydrogen bonds       : angle       4.57031 ( 1197)
  SS BOND              : bond        0.00565 (   12)
  SS BOND              : angle       1.24531 (   24)
  covalent geometry    : bond        0.00311 ( 9149)
  covalent geometry    : angle       0.68717 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 179
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8439 (tp) cc_final: 0.8099 (tt)
REVERT: A  128 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7900 (m-30)
REVERT: A  226 GLU cc_start: 0.8380 (pt0) cc_final: 0.7777 (pt0)
REVERT: H   26 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6101 (m-10)
REVERT: B   81 ASP cc_start: 0.8866 (p0) cc_final: 0.8653 (p0)
REVERT: B   95 TRP cc_start: 0.5554 (OUTLIER) cc_final: 0.4015 (t60)
REVERT: B  120 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7542 (mtt90)
REVERT: B  171 GLU cc_start: 0.7741 (tt0) cc_final: 0.7397 (tt0)
REVERT: B  185 CYS cc_start: 0.7647 (t) cc_final: 0.7302 (t)
REVERT: E  296 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (pt)
REVERT: F  255 TYR cc_start: 0.7603 (p90) cc_final: 0.7249 (p90)
  outliers start: 41
  outliers final: 27
  residues processed: 205
  average time/residue: 0.1992
  time to fit residues: 56.6454
Evaluate side-chains
  202 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  167 ILE
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  204 VAL
Chi-restraints excluded: chain E residue  296 ILE
Chi-restraints excluded: chain E residue  314 VAL
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  392 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0370
   chunk 80 optimal weight:    8.9990
   chunk 102 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 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 = 0.4112 r_free = 0.4112 target = 0.161652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.131113 restraints weight = 15491.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.133232 restraints weight = 9940.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.135103 restraints weight = 7293.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9184  Z= 0.159
  Angle     :  0.728   8.755  12536  Z= 0.354
  Chirality :  0.047   0.358   1510
  Planarity :  0.004   0.061   1519
  Dihedral  : 11.229 103.826   1627
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.06 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.83 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.27), residues: 1072
  helix:  1.50 (0.31), residues: 266
  sheet:  0.03 (0.28), residues: 371
  loop : -1.28 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP E 135 
 HIS   0.005   0.001   HIS E 396 
 PHE   0.015   0.001   PHE E 335 
 TYR   0.017   0.001   TYR G  43 
 ARG   0.006   0.001   ARG B  43 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00690 (   11)
  link_NAG-ASN         : angle       3.90898 (   33)
  link_ALPHA1-6        : bond        0.00416 (    2)
  link_ALPHA1-6        : angle       2.55323 (    6)
  link_BETA1-4         : bond        0.00412 (    8)
  link_BETA1-4         : angle       2.43942 (   24)
  link_ALPHA1-3        : bond        0.01000 (    2)
  link_ALPHA1-3        : angle       1.49707 (    6)
  hydrogen bonds       : bond        0.04028 (  420)
  hydrogen bonds       : angle       4.53090 ( 1197)
  SS BOND              : bond        0.00471 (   12)
  SS BOND              : angle       1.17621 (   24)
  covalent geometry    : bond        0.00367 ( 9149)
  covalent geometry    : angle       0.68909 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8529 (tp) cc_final: 0.8230 (tt)
REVERT: A  128 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7722 (m-30)
REVERT: A  226 GLU cc_start: 0.8340 (pt0) cc_final: 0.7735 (pt0)
REVERT: H   26 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6152 (m-10)
REVERT: H   29 ASP cc_start: 0.8231 (m-30) cc_final: 0.7819 (m-30)
REVERT: B   81 ASP cc_start: 0.8899 (p0) cc_final: 0.8699 (p0)
REVERT: B   95 TRP cc_start: 0.5712 (OUTLIER) cc_final: 0.4043 (t60)
REVERT: B  120 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7539 (mtt90)
REVERT: B  171 GLU cc_start: 0.7800 (tt0) cc_final: 0.7508 (tt0)
REVERT: B  176 MET cc_start: 0.7839 (mtm) cc_final: 0.7623 (mtm)
REVERT: B  185 CYS cc_start: 0.7573 (t) cc_final: 0.7208 (t)
REVERT: E  345 LEU cc_start: 0.8180 (mt) cc_final: 0.7937 (tp)
REVERT: F  222 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8500 (Cg_endo)
REVERT: F  255 TYR cc_start: 0.7687 (p90) cc_final: 0.7355 (p90)
REVERT: F  362 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6489 (mp)
  outliers start: 41
  outliers final: 26
  residues processed: 206
  average time/residue: 0.2257
  time to fit residues: 65.1021
Evaluate side-chains
  203 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  167 ILE
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  204 VAL
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  258 HIS
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  362 LEU
Chi-restraints excluded: chain F residue  392 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 63 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 102 optimal weight:    0.5980
   chunk 69 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 365 ASN
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.162251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131583 restraints weight = 15535.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.134055 restraints weight = 9827.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.134985 restraints weight = 6937.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9184  Z= 0.144
  Angle     :  0.749  14.184  12536  Z= 0.356
  Chirality :  0.047   0.354   1510
  Planarity :  0.004   0.062   1519
  Dihedral  : 10.723 100.643   1627
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.97 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 22.03 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.27), residues: 1072
  helix:  1.38 (0.31), residues: 273
  sheet:  0.05 (0.28), residues: 368
  loop : -1.32 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP E 135 
 HIS   0.004   0.001   HIS E 396 
 PHE   0.017   0.001   PHE E 178 
 TYR   0.028   0.002   TYR G  43 
 ARG   0.006   0.001   ARG G  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00647 (   11)
  link_NAG-ASN         : angle       3.62022 (   33)
  link_ALPHA1-6        : bond        0.00562 (    2)
  link_ALPHA1-6        : angle       2.50177 (    6)
  link_BETA1-4         : bond        0.00478 (    8)
  link_BETA1-4         : angle       2.29743 (   24)
  link_ALPHA1-3        : bond        0.01060 (    2)
  link_ALPHA1-3        : angle       1.40801 (    6)
  hydrogen bonds       : bond        0.04060 (  420)
  hydrogen bonds       : angle       4.51441 ( 1197)
  SS BOND              : bond        0.00544 (   12)
  SS BOND              : angle       1.26896 (   24)
  covalent geometry    : bond        0.00327 ( 9149)
  covalent geometry    : angle       0.71616 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8492 (tp) cc_final: 0.8276 (tt)
REVERT: A  128 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7808 (m-30)
REVERT: A  226 GLU cc_start: 0.8149 (pt0) cc_final: 0.7556 (pt0)
REVERT: H   26 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.5985 (m-10)
REVERT: H   29 ASP cc_start: 0.8205 (m-30) cc_final: 0.7814 (m-30)
REVERT: B   81 ASP cc_start: 0.8874 (p0) cc_final: 0.8505 (p0)
REVERT: B   83 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7310 (pm20)
REVERT: B   95 TRP cc_start: 0.5641 (OUTLIER) cc_final: 0.3944 (t60)
REVERT: B  120 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7415 (mtt90)
REVERT: B  144 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  185 CYS cc_start: 0.7560 (t) cc_final: 0.7241 (t)
REVERT: E  319 GLU cc_start: 0.6014 (tp30) cc_final: 0.5350 (tp30)
REVERT: F  222 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.8311 (Cg_endo)
REVERT: F  230 ASP cc_start: 0.8067 (m-30) cc_final: 0.7774 (m-30)
REVERT: F  255 TYR cc_start: 0.7640 (p90) cc_final: 0.7391 (p90)
REVERT: F  269 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8532 (mt)
  outliers start: 43
  outliers final: 34
  residues processed: 204
  average time/residue: 0.2036
  time to fit residues: 58.0020
Evaluate side-chains
  206 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  107 SER
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  258 HIS
Chi-restraints excluded: chain F residue  269 ILE
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  392 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 GLN
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.157956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.127484 restraints weight = 15574.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.128708 restraints weight = 9792.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129442 restraints weight = 8238.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   9184  Z= 0.201
  Angle     :  0.778  11.096  12536  Z= 0.374
  Chirality :  0.048   0.345   1510
  Planarity :  0.004   0.063   1519
  Dihedral  : 11.021  98.551   1627
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.62 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 21.93 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1072
  helix:  1.23 (0.31), residues: 269
  sheet: -0.05 (0.28), residues: 368
  loop : -1.31 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E 135 
 HIS   0.004   0.001   HIS F 396 
 PHE   0.015   0.002   PHE A 207 
 TYR   0.022   0.002   TYR G  43 
 ARG   0.007   0.001   ARG B  43 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00605 (   11)
  link_NAG-ASN         : angle       3.93811 (   33)
  link_ALPHA1-6        : bond        0.00317 (    2)
  link_ALPHA1-6        : angle       2.77885 (    6)
  link_BETA1-4         : bond        0.00429 (    8)
  link_BETA1-4         : angle       2.40570 (   24)
  link_ALPHA1-3        : bond        0.00838 (    2)
  link_ALPHA1-3        : angle       1.47782 (    6)
  hydrogen bonds       : bond        0.04314 (  420)
  hydrogen bonds       : angle       4.68349 ( 1197)
  SS BOND              : bond        0.00494 (   12)
  SS BOND              : angle       1.33682 (   24)
  covalent geometry    : bond        0.00474 ( 9149)
  covalent geometry    : angle       0.74126 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 172
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 GLU cc_start: 0.8225 (pt0) cc_final: 0.7766 (pt0)
REVERT: H   26 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6249 (m-10)
REVERT: B   81 ASP cc_start: 0.8927 (p0) cc_final: 0.8592 (p0)
REVERT: B   83 GLU cc_start: 0.7879 (pm20) cc_final: 0.7547 (pm20)
REVERT: B   95 TRP cc_start: 0.5880 (OUTLIER) cc_final: 0.4411 (t60)
REVERT: B  144 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8880 (mm)
REVERT: B  171 GLU cc_start: 0.8079 (tt0) cc_final: 0.7867 (tt0)
REVERT: B  185 CYS cc_start: 0.7702 (t) cc_final: 0.7398 (t)
REVERT: E  319 GLU cc_start: 0.6224 (tp30) cc_final: 0.5829 (tp30)
REVERT: E  345 LEU cc_start: 0.8091 (mt) cc_final: 0.7716 (tp)
REVERT: F  255 TYR cc_start: 0.7766 (p90) cc_final: 0.7472 (p90)
REVERT: F  362 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6655 (mp)
  outliers start: 57
  outliers final: 39
  residues processed: 210
  average time/residue: 0.2060
  time to fit residues: 60.1650
Evaluate side-chains
  207 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  179 ARG
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   46 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  167 ILE
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  204 VAL
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain E residue  408 THR
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  236 ASN
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  269 ILE
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  362 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 85 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 GLN
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.159912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129282 restraints weight = 15746.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.130111 restraints weight = 9466.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.130768 restraints weight = 8232.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9184  Z= 0.155
  Angle     :  0.777  14.870  12536  Z= 0.367
  Chirality :  0.047   0.344   1510
  Planarity :  0.004   0.063   1519
  Dihedral  : 10.545  96.202   1627
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.81 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.55 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.27), residues: 1072
  helix:  1.32 (0.31), residues: 269
  sheet: -0.03 (0.28), residues: 366
  loop : -1.24 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP E 135 
 HIS   0.004   0.001   HIS E 396 
 PHE   0.015   0.001   PHE E 178 
 TYR   0.023   0.001   TYR G  43 
 ARG   0.005   0.001   ARG B 194 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00632 (   11)
  link_NAG-ASN         : angle       3.63201 (   33)
  link_ALPHA1-6        : bond        0.00526 (    2)
  link_ALPHA1-6        : angle       2.49816 (    6)
  link_BETA1-4         : bond        0.00498 (    8)
  link_BETA1-4         : angle       2.17934 (   24)
  link_ALPHA1-3        : bond        0.01088 (    2)
  link_ALPHA1-3        : angle       1.35756 (    6)
  hydrogen bonds       : bond        0.04216 (  420)
  hydrogen bonds       : angle       4.63897 ( 1197)
  SS BOND              : bond        0.00891 (   12)
  SS BOND              : angle       1.16524 (   24)
  covalent geometry    : bond        0.00360 ( 9149)
  covalent geometry    : angle       0.74703 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 171
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8544 (tp) cc_final: 0.8216 (tt)
REVERT: A  226 GLU cc_start: 0.8168 (pt0) cc_final: 0.7680 (pt0)
REVERT: G   52 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8064 (pttp)
REVERT: H   26 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6117 (m-10)
REVERT: H   29 ASP cc_start: 0.8410 (m-30) cc_final: 0.8060 (m-30)
REVERT: B   81 ASP cc_start: 0.8855 (p0) cc_final: 0.8530 (p0)
REVERT: B   83 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7407 (pm20)
REVERT: B   95 TRP cc_start: 0.5802 (OUTLIER) cc_final: 0.4332 (t60)
REVERT: B  144 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (mm)
REVERT: B  185 CYS cc_start: 0.7415 (t) cc_final: 0.7179 (t)
REVERT: E  319 GLU cc_start: 0.5981 (tp30) cc_final: 0.5602 (tp30)
REVERT: F  255 TYR cc_start: 0.7723 (p90) cc_final: 0.7430 (p90)
REVERT: F  362 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6581 (mp)
  outliers start: 40
  outliers final: 31
  residues processed: 193
  average time/residue: 0.1996
  time to fit residues: 53.3589
Evaluate side-chains
  198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  226 CYS
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  258 HIS
Chi-restraints excluded: chain F residue  269 ILE
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  362 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 76 optimal weight:    0.2980
   chunk 98 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 114 HIS
** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.155434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.124423 restraints weight = 15676.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125432 restraints weight = 10203.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126155 restraints weight = 8434.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.4969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9184  Z= 0.237
  Angle     :  0.855  13.024  12536  Z= 0.404
  Chirality :  0.050   0.338   1510
  Planarity :  0.004   0.066   1519
  Dihedral  : 10.996  95.040   1627
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  7.65 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 22.84 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.26), residues: 1072
  helix:  1.25 (0.31), residues: 269
  sheet: -0.27 (0.27), residues: 368
  loop : -1.33 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 135 
 HIS   0.005   0.001   HIS F 396 
 PHE   0.020   0.002   PHE E 178 
 TYR   0.042   0.002   TYR B 193 
 ARG   0.008   0.001   ARG B  43 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00584 (   11)
  link_NAG-ASN         : angle       4.03437 (   33)
  link_ALPHA1-6        : bond        0.00213 (    2)
  link_ALPHA1-6        : angle       2.80974 (    6)
  link_BETA1-4         : bond        0.00498 (    8)
  link_BETA1-4         : angle       2.44505 (   24)
  link_ALPHA1-3        : bond        0.01071 (    2)
  link_ALPHA1-3        : angle       1.66952 (    6)
  hydrogen bonds       : bond        0.04517 (  420)
  hydrogen bonds       : angle       4.82429 ( 1197)
  SS BOND              : bond        0.00814 (   12)
  SS BOND              : angle       1.50580 (   24)
  covalent geometry    : bond        0.00561 ( 9149)
  covalent geometry    : angle       0.81953 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   49 GLN cc_start: 0.8227 (pt0) cc_final: 0.7950 (pt0)
REVERT: H   26 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6338 (m-10)
REVERT: B   81 ASP cc_start: 0.8898 (p0) cc_final: 0.8591 (p0)
REVERT: B   83 GLU cc_start: 0.7868 (pm20) cc_final: 0.7458 (pm20)
REVERT: B   95 TRP cc_start: 0.6313 (OUTLIER) cc_final: 0.4817 (t60)
REVERT: B  171 GLU cc_start: 0.8149 (tt0) cc_final: 0.7752 (tt0)
REVERT: B  185 CYS cc_start: 0.7800 (t) cc_final: 0.7565 (t)
REVERT: E  319 GLU cc_start: 0.6131 (tp30) cc_final: 0.5719 (tp30)
REVERT: E  345 LEU cc_start: 0.8023 (mt) cc_final: 0.7698 (tp)
REVERT: F  137 MET cc_start: 0.7252 (ttt) cc_final: 0.7031 (ttt)
REVERT: F  255 TYR cc_start: 0.7864 (p90) cc_final: 0.7526 (p90)
REVERT: F  362 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6759 (mp)
  outliers start: 41
  outliers final: 33
  residues processed: 200
  average time/residue: 0.2084
  time to fit residues: 57.5589
Evaluate side-chains
  203 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   42 LEU
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  175 MET
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  226 CYS
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  272 VAL
Chi-restraints excluded: chain E residue  303 THR
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  258 HIS
Chi-restraints excluded: chain F residue  269 ILE
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  362 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 65 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0370
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0570
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  65 HIS
B 126 ASN
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.159957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.128604 restraints weight = 15692.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130548 restraints weight = 10847.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.132109 restraints weight = 8051.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9184  Z= 0.143
  Angle     :  0.804  14.691  12536  Z= 0.377
  Chirality :  0.049   0.336   1510
  Planarity :  0.004   0.063   1519
  Dihedral  : 10.317  93.456   1627
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.44 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.77 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.27), residues: 1072
  helix:  1.25 (0.31), residues: 269
  sheet: -0.10 (0.28), residues: 369
  loop : -1.29 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 254 
 HIS   0.005   0.001   HIS E 105 
 PHE   0.021   0.001   PHE E 178 
 TYR   0.031   0.002   TYR B 193 
 ARG   0.015   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (   11)
  link_NAG-ASN         : angle       3.55607 (   33)
  link_ALPHA1-6        : bond        0.00678 (    2)
  link_ALPHA1-6        : angle       2.44187 (    6)
  link_BETA1-4         : bond        0.00576 (    8)
  link_BETA1-4         : angle       2.07509 (   24)
  link_ALPHA1-3        : bond        0.01117 (    2)
  link_ALPHA1-3        : angle       1.31358 (    6)
  hydrogen bonds       : bond        0.04452 (  420)
  hydrogen bonds       : angle       4.67531 ( 1197)
  SS BOND              : bond        0.00640 (   12)
  SS BOND              : angle       1.09312 (   24)
  covalent geometry    : bond        0.00321 ( 9149)
  covalent geometry    : angle       0.77646 (12443)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.8474 (tp) cc_final: 0.8160 (tt)
REVERT: H   26 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6170 (m-10)
REVERT: B   81 ASP cc_start: 0.8819 (p0) cc_final: 0.8558 (p0)
REVERT: B   83 GLU cc_start: 0.7798 (pm20) cc_final: 0.7391 (pm20)
REVERT: B   95 TRP cc_start: 0.6043 (OUTLIER) cc_final: 0.4472 (t60)
REVERT: B  181 ILE cc_start: 0.9075 (mt) cc_final: 0.8713 (mm)
REVERT: E  319 GLU cc_start: 0.5935 (tp30) cc_final: 0.5589 (tp30)
REVERT: E  326 ARG cc_start: 0.8057 (mmp80) cc_final: 0.7710 (mmp80)
REVERT: F  255 TYR cc_start: 0.7752 (p90) cc_final: 0.7434 (p90)
  outliers start: 30
  outliers final: 25
  residues processed: 195
  average time/residue: 0.1974
  time to fit residues: 53.6723
Evaluate side-chains
  196 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   26 TYR
Chi-restraints excluded: chain H residue   44 CYS
Chi-restraints excluded: chain B residue   95 TRP
Chi-restraints excluded: chain B residue  152 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain E residue  103 LEU
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  226 CYS
Chi-restraints excluded: chain E residue  228 VAL
Chi-restraints excluded: chain E residue  375 SER
Chi-restraints excluded: chain E residue  379 VAL
Chi-restraints excluded: chain F residue  114 HIS
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  168 THR
Chi-restraints excluded: chain F residue  173 MET
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  241 TRP
Chi-restraints excluded: chain F residue  256 THR
Chi-restraints excluded: chain F residue  258 HIS
Chi-restraints excluded: chain F residue  269 ILE
Chi-restraints excluded: chain F residue  303 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0470
   chunk 103 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 GLN
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.159956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.129499 restraints weight = 15687.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130963 restraints weight = 9740.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132599 restraints weight = 8013.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.5093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9184  Z= 0.149
  Angle     :  0.825  16.584  12536  Z= 0.384
  Chirality :  0.048   0.331   1510
  Planarity :  0.004   0.065   1519
  Dihedral  : 10.063  89.076   1627
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  7.09 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 25.69 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.26), residues: 1072
  helix:  1.24 (0.31), residues: 269
  sheet: -0.04 (0.28), residues: 364
  loop : -1.26 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 135 
 HIS   0.004   0.001   HIS E 105 
 PHE   0.019   0.001   PHE E 178 
 TYR   0.021   0.002   TYR G  43 
 ARG   0.011   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00600 (   11)
  link_NAG-ASN         : angle       3.50476 (   33)
  link_ALPHA1-6        : bond        0.00618 (    2)
  link_ALPHA1-6        : angle       2.40707 (    6)
  link_BETA1-4         : bond        0.00515 (    8)
  link_BETA1-4         : angle       2.09493 (   24)
  link_ALPHA1-3        : bond        0.01012 (    2)
  link_ALPHA1-3        : angle       1.40865 (    6)
  hydrogen bonds       : bond        0.04421 (  420)
  hydrogen bonds       : angle       4.61694 ( 1197)
  SS BOND              : bond        0.00628 (   12)
  SS BOND              : angle       1.04033 (   24)
  covalent geometry    : bond        0.00348 ( 9149)
  covalent geometry    : angle       0.79876 (12443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2876.10 seconds
wall clock time: 51 minutes 19.96 seconds (3079.96 seconds total)