Starting phenix.real_space_refine
on Thu Jul  2 12:16:30 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ejc_28177/07_2026/8ejc_28177.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      50      5.16       5
     C    5506      2.51       5
     N    1489      2.21       5
     O    1614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8659
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1877
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2572
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "C"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 406
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "E"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 1983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1983
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 20, 'TRANS': 250}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "R"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'2YB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.80, per 1000 atoms: 0.21
  Number of scatterers: 8659
  At special positions: 0
  Unit cell: (96.3, 115.56, 129.47, 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      50     16.00
     O    1614      8.00
     N    1489      7.00
     C    5506      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.04

  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
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 548.3 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      39.0% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 4.324A  pdb=" N   THR A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.918A  pdb=" N   ILE A  49 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 93
      removed outlier: 3.737A  pdb=" N   ASN A  93 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 122
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 3.870A  pdb=" N   PHE A 156 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.040A  pdb=" N   ARG A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 195
      removed outlier: 3.620A  pdb=" N   PHE A 189 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 235
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.915A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 7 through 28
      removed outlier: 4.306A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.137A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.582A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 37
      Proline residue:  R  21  - end of helix
      removed outlier: 4.197A  pdb=" N   LEU R  36 " --> pdb=" O   ALA R  32 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG R  37 " --> pdb=" O   HIS R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 68
      Proline residue:  R  60  - end of helix
    Processing helix  chain 'R' and resid 75 through 77
      No H-bonds generated for 'chain 'R' and resid 75 through 77'
    Processing helix  chain 'R' and resid 78 through 110
      Proline residue:  R  89  - end of helix
    Processing helix  chain 'R' and resid 110 through 117
    Processing helix  chain 'R' and resid 119 through 144
      removed outlier: 3.683A  pdb=" N   SER R 123 " --> pdb=" O   ARG R 119 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU R 144 " --> pdb=" O   LEU R 140 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 212
      Proline residue:  R 181  - end of helix
      removed outlier: 4.919A  pdb=" N   LEU R 193 " --> pdb=" O   LEU R 189 " (cutoff:3.500A)
      Proline residue:  R 194  - end of helix
    Processing helix  chain 'R' and resid 215 through 235
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 3.875A  pdb=" N   TYR R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 277
      removed outlier: 3.801A  pdb=" N   LYS R 259 " --> pdb=" O   GLY R 255 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   VAL R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68
      removed outlier: 3.820A  pdb=" N   ALA A  97 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.179A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.598A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.515A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.535A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.727A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.540A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.506A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.546A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149
      removed outlier: 3.893A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1284 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: 1.42

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2831
        1.34 -     1.46: 2186
        1.46 -     1.58: 3770
        1.58 -     1.71: 0
        1.71 -     1.83: 68
  Bond restraints: 8855
  Sorted by residual:
  bond pdb=" C27 2YB R 401 "
       pdb=" C28 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.505  1.384  0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" C1  2YB R 401 "
       pdb=" C2  2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.391  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C14 2YB R 401 "
       pdb=" C15 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.390  0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" C21 2YB R 401 "
       pdb=" C22 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.498  1.391  0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C16 2YB R 401 "
       pdb=" C17 2YB R 401 "
    ideal  model  delta    sigma   weight residual
    1.485  1.394  0.091 2.00e-02 2.50e+03 2.05e+01
  ... (remaining 8850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 11699
        1.62 -     3.25: 281
        3.25 -     4.87: 42
        4.87 -     6.50: 14
        6.50 -     8.12: 6
  Bond angle restraints: 12042
  Sorted by residual:
  angle pdb=" CA  TRP R 131 "
        pdb=" CB  TRP R 131 "
        pdb=" CG  TRP R 131 "
      ideal   model   delta    sigma   weight residual
     113.60  119.94   -6.34 1.90e+00 2.77e-01 1.11e+01
  angle pdb=" O11 2YB R 401 "
        pdb=" S9  2YB R 401 "
        pdb=" O12 2YB R 401 "
      ideal   model   delta    sigma   weight residual
     117.70  109.58    8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" N   GLU A 171 "
        pdb=" CA  GLU A 171 "
        pdb=" C   GLU A 171 "
      ideal   model   delta    sigma   weight residual
     109.81  115.39   -5.58 2.21e+00 2.05e-01 6.37e+00
  angle pdb=" C22 2YB R 401 "
        pdb=" O23 2YB R 401 "
        pdb=" C24 2YB R 401 "
      ideal   model   delta    sigma   weight residual
     118.60  111.15    7.45 3.00e+00 1.11e-01 6.17e+00
  angle pdb=" C   TYR B  59 "
        pdb=" N   ALA B  60 "
        pdb=" CA  ALA B  60 "
      ideal   model   delta    sigma   weight residual
     121.85  117.88    3.97 1.77e+00 3.19e-01 5.03e+00
  ... (remaining 12037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.52: 4955
       24.52 -    49.04: 220
       49.04 -    73.56: 16
       73.56 -    98.08: 3
       98.08 -   122.60: 1
  Dihedral angle restraints: 5195
    sinusoidal: 1945
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  GLY B 141 "
           pdb=" C   GLY B 141 "
           pdb=" N   HIS B 142 "
           pdb=" CA  HIS B 142 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.09   20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  GLY B 182 "
           pdb=" C   GLY B 182 "
           pdb=" N   HIS B 183 "
           pdb=" CA  HIS B 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.70   20.30     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C8  2YB R 401 "
           pdb=" C6  2YB R 401 "
           pdb=" C7  2YB R 401 "
           pdb=" O5  2YB R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.08   57.48  122.60     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 5192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 824
       0.034 -    0.068: 367
       0.068 -    0.102: 113
       0.102 -    0.136: 48
       0.136 -    0.170: 4
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CB  THR E 172 "
            pdb=" CA  THR E 172 "
            pdb=" OG1 THR E 172 "
            pdb=" CG2 THR E 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.24e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CG  LEU R  11 "
            pdb=" CB  LEU R  11 "
            pdb=" CD1 LEU R  11 "
            pdb=" CD2 LEU R  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 238 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO R 239 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 239 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 239 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 131 "    0.014 2.00e-02 2.50e+03   1.07e-02 2.86e+00
        pdb=" CG  TRP R 131 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 131 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 131 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 131 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 131 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 131 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 131 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 131 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 131 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO B 236 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 851
        2.74 -     3.28: 8711
        3.28 -     3.82: 14578
        3.82 -     4.36: 17216
        4.36 -     4.90: 29793
  Nonbonded interactions: 71149
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  15 "
            pdb=" O   VAL B  90 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OE2 GLU A 234 "
            pdb=" NH1 ARG R 118 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER C  57 "
            pdb=" OE1 GLU C  58 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.317 3.040
  ... (remaining 71144 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.090
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.121   8856  Z= 0.252
  Angle     :  0.645   8.121  12044  Z= 0.323
  Chirality :  0.044   0.170   1356
  Planarity :  0.004   0.052   1543
  Dihedral  : 13.248 122.600   3106
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.26), residues: 1118
  helix:  2.17 (0.26), residues: 375
  sheet:  0.40 (0.32), residues: 294
  loop : -0.02 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  72 
 TYR   0.017   0.002   TYR B 105 
 PHE   0.014   0.002   PHE B 253 
 TRP   0.029   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00557 /  0.25 ( 8855)
  covalent geometry    : angle       0.64459 /  0.32 (12042)
  SS BOND              : bond        0.00644 /  0.34 (    1)
  SS BOND              : angle       0.69569 /  0.38 (    2)
  hydrogen bonds       : bond        0.13729 /  9.71 (  456)
  hydrogen bonds       : angle       5.74050 /  3.96 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: C   32 LYS cc_start: 0.8887 (tttm) cc_final: 0.8540 (tttm)
REVERT: E   93 MET cc_start: 0.7849 (tpt) cc_final: 0.7597 (tpt)
REVERT: E  201 ASP cc_start: 0.7962 (p0) cc_final: 0.7738 (t70)
REVERT: R  137 HIS cc_start: 0.8206 (t-90) cc_final: 0.7843 (t-90)
REVERT: R  170 CYS cc_start: 0.7786 (m) cc_final: 0.7585 (m)
REVERT: R  240 TYR cc_start: 0.8514 (t80) cc_final: 0.8231 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.5863
  time to fit residues: 100.2729
Evaluate side-chains
  117 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.0770
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    1.7142

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  16 ASN
B  36 ASN
E  77 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.111036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.082670 restraints weight = 15679.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.65
r_work: 0.2994 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8856  Z= 0.154
  Angle     :  0.585   7.354  12044  Z= 0.302
  Chirality :  0.042   0.129   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  5.415  89.013   1236
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.18 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.25), residues: 1118
  helix:  2.27 (0.26), residues: 381
  sheet:  0.55 (0.33), residues: 282
  loop : -0.06 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 160 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.025   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 8855)
  covalent geometry    : angle       0.58471 /  0.30 (12042)
  SS BOND              : bond        0.00591 /  0.31 (    1)
  SS BOND              : angle       0.50279 /  0.27 (    2)
  hydrogen bonds       : bond        0.04444 /  3.06 (  456)
  hydrogen bonds       : angle       4.64021 /  3.26 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7578 (mt-10)
REVERT: B   16 ASN cc_start: 0.8707 (m-40) cc_final: 0.8297 (m110)
REVERT: B   20 ASP cc_start: 0.8263 (m-30) cc_final: 0.8002 (m-30)
REVERT: B  175 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8320 (mp10)
REVERT: E   93 MET cc_start: 0.8652 (tpt) cc_final: 0.8181 (tpt)
REVERT: E  201 ASP cc_start: 0.8561 (p0) cc_final: 0.7951 (t70)
REVERT: R   53 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8706 (tp)
REVERT: R  137 HIS cc_start: 0.8236 (t-90) cc_final: 0.7798 (t-90)
REVERT: R  161 ASN cc_start: 0.8362 (t0) cc_final: 0.8078 (t0)
REVERT: R  170 CYS cc_start: 0.8067 (m) cc_final: 0.7780 (m)
REVERT: R  221 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6698 (ttm170)
REVERT: R  240 TYR cc_start: 0.8717 (t80) cc_final: 0.8347 (t80)
  outliers start: 16
  outliers final: 5
  residues processed: 139
  average time/residue: 0.5079
  time to fit residues: 75.3933
Evaluate side-chains
  129 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  232 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    0.1980
   chunk 71 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  36 ASN
E  77 ASN
R  23 ASN
R  47 ASN
R 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.110401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.082166 restraints weight = 15563.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.63
r_work: 0.2981 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8856  Z= 0.167
  Angle     :  0.572   7.420  12044  Z= 0.296
  Chirality :  0.042   0.129   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.301  77.062   1236
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 13.73 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.25), residues: 1118
  helix:  2.26 (0.27), residues: 377
  sheet:  0.60 (0.33), residues: 273
  loop : -0.17 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 160 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.024   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 ( 8855)
  covalent geometry    : angle       0.57214 /  0.30 (12042)
  SS BOND              : bond        0.00559 /  0.29 (    1)
  SS BOND              : angle       0.47300 /  0.25 (    2)
  hydrogen bonds       : bond        0.04337 /  2.99 (  456)
  hydrogen bonds       : angle       4.50591 /  3.17 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8270 (m-30) cc_final: 0.8063 (m-30)
REVERT: B  175 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8299 (mp10)
REVERT: B  254 ASP cc_start: 0.8703 (t0) cc_final: 0.8487 (t0)
REVERT: E   19 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8783 (tttm)
REVERT: E   51 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8784 (tp)
REVERT: E   93 MET cc_start: 0.8607 (tpt) cc_final: 0.8134 (tpt)
REVERT: E  109 ASP cc_start: 0.8666 (p0) cc_final: 0.8380 (p0)
REVERT: E  118 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6636 (m)
REVERT: R   23 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8709 (t0)
REVERT: R   52 ASP cc_start: 0.8737 (t70) cc_final: 0.8440 (t70)
REVERT: R   53 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8769 (tp)
REVERT: R  137 HIS cc_start: 0.8186 (t-90) cc_final: 0.7785 (t-90)
REVERT: R  161 ASN cc_start: 0.8208 (t0) cc_final: 0.7866 (t0)
REVERT: R  170 CYS cc_start: 0.7997 (m) cc_final: 0.7684 (m)
REVERT: R  221 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6716 (ttm170)
  outliers start: 35
  outliers final: 14
  residues processed: 144
  average time/residue: 0.5642
  time to fit residues: 86.5020
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
A 229 GLN
B  35 ASN
B  75 GLN
C  44 HIS
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.110707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.082432 restraints weight = 15850.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 2.65
r_work: 0.2989 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8856  Z= 0.150
  Angle     :  0.565   9.617  12044  Z= 0.289
  Chirality :  0.042   0.133   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.180  69.812   1236
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.83 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1118
  helix:  2.21 (0.26), residues: 384
  sheet:  0.62 (0.32), residues: 289
  loop : -0.14 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 160 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.024   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 8855)
  covalent geometry    : angle       0.56496 /  0.29 (12042)
  SS BOND              : bond        0.00524 /  0.28 (    1)
  SS BOND              : angle       0.45005 /  0.24 (    2)
  hydrogen bonds       : bond        0.04148 /  2.85 (  456)
  hydrogen bonds       : angle       4.43485 /  3.11 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7576 (mt-10)
REVERT: B   20 ASP cc_start: 0.8235 (m-30) cc_final: 0.7973 (m-30)
REVERT: B  175 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (mp10)
REVERT: B  215 GLU cc_start: 0.8132 (pt0) cc_final: 0.7888 (pp20)
REVERT: B  217 MET cc_start: 0.8055 (pp-130) cc_final: 0.7345 (pp-130)
REVERT: B  254 ASP cc_start: 0.8735 (t0) cc_final: 0.8521 (t0)
REVERT: E   19 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8774 (tttm)
REVERT: E   51 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8765 (tp)
REVERT: E  118 THR cc_start: 0.6944 (OUTLIER) cc_final: 0.6724 (m)
REVERT: R   23 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8656 (t0)
REVERT: R   52 ASP cc_start: 0.8794 (t70) cc_final: 0.8470 (t70)
REVERT: R   53 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8770 (tp)
REVERT: R  137 HIS cc_start: 0.8159 (t-90) cc_final: 0.7787 (t-90)
REVERT: R  161 ASN cc_start: 0.8291 (t0) cc_final: 0.7886 (t0)
REVERT: R  170 CYS cc_start: 0.7935 (m) cc_final: 0.7655 (m)
REVERT: R  221 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6691 (ttm170)
REVERT: R  240 TYR cc_start: 0.8648 (t80) cc_final: 0.8316 (t80)
  outliers start: 34
  outliers final: 14
  residues processed: 143
  average time/residue: 0.5723
  time to fit residues: 87.2381
Evaluate side-chains
  141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
B 220 GLN
R  23 ASN
R  47 ASN
R 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.111491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.083270 restraints weight = 15830.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.65
r_work: 0.3000 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8856  Z= 0.131
  Angle     :  0.556   9.095  12044  Z= 0.285
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.036  63.025   1236
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.72 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1118
  helix:  2.24 (0.26), residues: 384
  sheet:  0.60 (0.33), residues: 285
  loop : -0.10 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 160 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.024   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 8855)
  covalent geometry    : angle       0.55586 /  0.29 (12042)
  SS BOND              : bond        0.00500 /  0.26 (    1)
  SS BOND              : angle       0.41660 /  0.22 (    2)
  hydrogen bonds       : bond        0.03940 /  2.70 (  456)
  hydrogen bonds       : angle       4.33448 /  3.04 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7544 (mt-10)
REVERT: B  175 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8366 (mp10)
REVERT: B  254 ASP cc_start: 0.8727 (t0) cc_final: 0.8494 (t0)
REVERT: E   19 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8800 (tttm)
REVERT: E   51 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8757 (tp)
REVERT: E  109 ASP cc_start: 0.8645 (p0) cc_final: 0.8426 (p0)
REVERT: E  160 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8231 (ttm110)
REVERT: R   23 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8710 (t0)
REVERT: R   52 ASP cc_start: 0.8823 (t70) cc_final: 0.8456 (t70)
REVERT: R   53 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8790 (tp)
REVERT: R   54 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8412 (tt)
REVERT: R  137 HIS cc_start: 0.8120 (t-90) cc_final: 0.7734 (t-90)
REVERT: R  161 ASN cc_start: 0.8217 (t0) cc_final: 0.7851 (t0)
REVERT: R  170 CYS cc_start: 0.7909 (m) cc_final: 0.7651 (m)
REVERT: R  221 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6882 (tpt170)
REVERT: R  240 TYR cc_start: 0.8661 (t80) cc_final: 0.8369 (t80)
  outliers start: 35
  outliers final: 12
  residues processed: 146
  average time/residue: 0.5422
  time to fit residues: 84.5597
Evaluate side-chains
  140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   54 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  221 ARG
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 106 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0020
   chunk 43 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.2392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
B  75 GLN
B 110 ASN
E  77 ASN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.111855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.083665 restraints weight = 15697.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.65
r_work: 0.3009 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8856  Z= 0.126
  Angle     :  0.561   8.822  12044  Z= 0.286
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.953  58.589   1236
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.83 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.26), residues: 1118
  helix:  2.23 (0.26), residues: 384
  sheet:  0.76 (0.33), residues: 278
  loop : -0.12 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 160 
 TYR   0.015   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.024   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 8855)
  covalent geometry    : angle       0.56125 /  0.29 (12042)
  SS BOND              : bond        0.00490 /  0.26 (    1)
  SS BOND              : angle       0.39460 /  0.21 (    2)
  hydrogen bonds       : bond        0.03849 /  2.64 (  456)
  hydrogen bonds       : angle       4.29609 /  3.02 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 126
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: B  175 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8374 (mp10)
REVERT: B  217 MET cc_start: 0.8215 (pp-130) cc_final: 0.7934 (pp-130)
REVERT: B  254 ASP cc_start: 0.8747 (t0) cc_final: 0.8514 (t0)
REVERT: E   19 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8798 (tttm)
REVERT: E   51 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: E  109 ASP cc_start: 0.8699 (p0) cc_final: 0.8467 (p0)
REVERT: R   23 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8694 (t0)
REVERT: R   52 ASP cc_start: 0.8799 (t70) cc_final: 0.8424 (t70)
REVERT: R   53 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8753 (tp)
REVERT: R  161 ASN cc_start: 0.8241 (t0) cc_final: 0.7880 (t0)
REVERT: R  170 CYS cc_start: 0.7851 (m) cc_final: 0.7630 (m)
  outliers start: 33
  outliers final: 13
  residues processed: 144
  average time/residue: 0.5495
  time to fit residues: 84.5850
Evaluate side-chains
  135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.112024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.083731 restraints weight = 15819.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.65
r_work: 0.3010 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8856  Z= 0.131
  Angle     :  0.574   8.122  12044  Z= 0.291
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.944  63.188   1236
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.16 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.26), residues: 1118
  helix:  2.17 (0.26), residues: 386
  sheet:  0.80 (0.33), residues: 282
  loop : -0.10 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 160 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.024   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 8855)
  covalent geometry    : angle       0.57398 /  0.29 (12042)
  SS BOND              : bond        0.00485 /  0.26 (    1)
  SS BOND              : angle       0.40250 /  0.21 (    2)
  hydrogen bonds       : bond        0.03835 /  2.63 (  456)
  hydrogen bonds       : angle       4.26106 /  3.00 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7576 (mt-10)
REVERT: B  175 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8378 (mp10)
REVERT: B  254 ASP cc_start: 0.8746 (t0) cc_final: 0.8499 (t0)
REVERT: E   19 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8797 (tttm)
REVERT: E   51 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8757 (tp)
REVERT: E  109 ASP cc_start: 0.8673 (p0) cc_final: 0.8403 (p0)
REVERT: E  160 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8207 (ttm110)
REVERT: R   53 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8760 (tp)
REVERT: R  137 HIS cc_start: 0.7991 (t70) cc_final: 0.7554 (t-90)
REVERT: R  161 ASN cc_start: 0.8220 (t0) cc_final: 0.7851 (t0)
REVERT: R  240 TYR cc_start: 0.8616 (t80) cc_final: 0.8388 (t80)
  outliers start: 30
  outliers final: 15
  residues processed: 141
  average time/residue: 0.5823
  time to fit residues: 87.4543
Evaluate side-chains
  136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0980
   chunk 26 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
E  77 ASN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.111784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.083634 restraints weight = 15684.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.64
r_work: 0.3011 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8856  Z= 0.136
  Angle     :  0.587   9.081  12044  Z= 0.296
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.948  66.190   1236
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.38 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1118
  helix:  2.14 (0.26), residues: 386
  sheet:  0.79 (0.32), residues: 281
  loop : -0.17 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 214 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.023   0.001   TRP R 131 
 HIS   0.005   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 8855)
  covalent geometry    : angle       0.58657 /  0.30 (12042)
  SS BOND              : bond        0.00474 /  0.25 (    1)
  SS BOND              : angle       0.41350 /  0.22 (    2)
  hydrogen bonds       : bond        0.03861 /  2.65 (  456)
  hydrogen bonds       : angle       4.26904 /  3.00 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: B   15 LYS cc_start: 0.8247 (mtmm) cc_final: 0.8018 (mtmm)
REVERT: B  254 ASP cc_start: 0.8743 (t0) cc_final: 0.8503 (t0)
REVERT: E   19 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8789 (tttm)
REVERT: E   51 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8762 (tp)
REVERT: E   93 MET cc_start: 0.8617 (tpt) cc_final: 0.8416 (tpt)
REVERT: E  109 ASP cc_start: 0.8649 (p0) cc_final: 0.8426 (p0)
REVERT: E  160 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8229 (ttm110)
REVERT: R   23 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8673 (t0)
REVERT: R   52 ASP cc_start: 0.8768 (t70) cc_final: 0.8379 (t70)
REVERT: R   53 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8759 (tp)
REVERT: R  137 HIS cc_start: 0.8000 (t70) cc_final: 0.7557 (t-90)
REVERT: R  161 ASN cc_start: 0.8230 (t0) cc_final: 0.7859 (t0)
REVERT: R  170 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7105 (m)
REVERT: R  240 TYR cc_start: 0.8659 (t80) cc_final: 0.8405 (t80)
  outliers start: 31
  outliers final: 15
  residues processed: 138
  average time/residue: 0.5751
  time to fit residues: 84.6935
Evaluate side-chains
  138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   36 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
B  35 ASN
B  75 GLN
E  77 ASN
R  23 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.083839 restraints weight = 15699.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.65
r_work: 0.3008 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8856  Z= 0.132
  Angle     :  0.584   8.326  12044  Z= 0.296
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.939  66.868   1236
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.15 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1118
  helix:  2.22 (0.26), residues: 380
  sheet:  0.74 (0.32), residues: 283
  loop : -0.18 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 160 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.023   0.001   TRP R 131 
 HIS   0.005   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 8855)
  covalent geometry    : angle       0.58383 /  0.30 (12042)
  SS BOND              : bond        0.00463 /  0.24 (    1)
  SS BOND              : angle       0.41284 /  0.22 (    2)
  hydrogen bonds       : bond        0.03820 /  2.62 (  456)
  hydrogen bonds       : angle       4.23719 /  2.98 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7601 (mt-10)
REVERT: B  254 ASP cc_start: 0.8749 (t0) cc_final: 0.8500 (t0)
REVERT: E   19 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8793 (tttm)
REVERT: E   51 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8754 (tp)
REVERT: E  109 ASP cc_start: 0.8675 (p0) cc_final: 0.8458 (p0)
REVERT: E  160 ARG cc_start: 0.8618 (mtp85) cc_final: 0.8252 (ttm110)
REVERT: R   53 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8763 (tp)
REVERT: R  137 HIS cc_start: 0.8186 (t70) cc_final: 0.7699 (t-90)
REVERT: R  161 ASN cc_start: 0.8285 (t0) cc_final: 0.7902 (t0)
REVERT: R  170 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7138 (m)
REVERT: R  240 TYR cc_start: 0.8670 (t80) cc_final: 0.8398 (t80)
  outliers start: 26
  outliers final: 15
  residues processed: 137
  average time/residue: 0.5587
  time to fit residues: 81.8329
Evaluate side-chains
  137 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0570
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 36 optimal weight:    0.2980
   overall best weight:    1.4702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
B  35 ASN
E  77 ASN
R  23 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.111757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.083591 restraints weight = 15734.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.65
r_work: 0.3010 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8856  Z= 0.139
  Angle     :  0.594   8.498  12044  Z= 0.302
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.973  67.969   1236
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.04 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1118
  helix:  2.21 (0.26), residues: 380
  sheet:  0.69 (0.32), residues: 286
  loop : -0.17 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 214 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.023   0.001   TRP R 131 
 HIS   0.005   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 8855)
  covalent geometry    : angle       0.59364 /  0.30 (12042)
  SS BOND              : bond        0.00476 /  0.25 (    1)
  SS BOND              : angle       0.40731 /  0.21 (    2)
  hydrogen bonds       : bond        0.03875 /  2.66 (  456)
  hydrogen bonds       : angle       4.25288 /  3.00 ( 1284)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7583 (mt-10)
REVERT: B  254 ASP cc_start: 0.8781 (t0) cc_final: 0.8537 (t0)
REVERT: E   19 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8786 (tttm)
REVERT: E   51 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8761 (tp)
REVERT: E  109 ASP cc_start: 0.8672 (p0) cc_final: 0.8459 (p0)
REVERT: E  160 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8260 (ttm110)
REVERT: R   23 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8678 (t0)
REVERT: R   52 ASP cc_start: 0.8790 (t70) cc_final: 0.8408 (t70)
REVERT: R   53 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: R  137 HIS cc_start: 0.8160 (t70) cc_final: 0.7741 (t-90)
REVERT: R  161 ASN cc_start: 0.8287 (t0) cc_final: 0.7906 (t0)
REVERT: R  170 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7150 (m)
REVERT: R  190 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8979 (mp)
REVERT: R  240 TYR cc_start: 0.8689 (t80) cc_final: 0.8423 (t80)
  outliers start: 27
  outliers final: 15
  residues processed: 138
  average time/residue: 0.5760
  time to fit residues: 84.8223
Evaluate side-chains
  139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain R residue   23 ASN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  170 CYS
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  220 LEU
Chi-restraints excluded: chain R residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 101 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 GLN
A 229 GLN
E  77 ASN
R  23 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.112476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.084351 restraints weight = 15642.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.64
r_work: 0.3023 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8856  Z= 0.126
  Angle     :  0.603   9.783  12044  Z= 0.305
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  4.942  68.613   1236
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.59 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.26), residues: 1118
  helix:  2.22 (0.26), residues: 380
  sheet:  0.81 (0.33), residues: 281
  loop : -0.20 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 214 
 TYR   0.013   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.024   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 8855)
  covalent geometry    : angle       0.60299 /  0.31 (12042)
  SS BOND              : bond        0.00459 /  0.24 (    1)
  SS BOND              : angle       0.39363 /  0.21 (    2)
  hydrogen bonds       : bond        0.03763 /  2.58 (  456)
  hydrogen bonds       : angle       4.24374 /  2.99 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3471.10 seconds
wall clock time: 60 minutes 3.11 seconds (3603.11 seconds total)