Starting phenix.real_space_refine
on Fri Aug 22 23:59:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ejc_28177/08_2025/8ejc_28177.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ejc_28177/08_2025/8ejc_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_28177/08_2025/8ejc_28177.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ejc_28177/08_2025/8ejc_28177.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ejc_28177/08_2025/8ejc_28177.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ejc_28177/08_2025/8ejc_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-2.0-5787/lib/python3.9/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: 1.51, per 1000 atoms: 0.17
  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: 0.58
  Conformation dependent library (CDL) restraints added in 321.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 1.16

  Time building geometry restraints manager: 0.84 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: 4962
       24.52 -    49.04: 224
       49.04 -    73.56: 18
       73.56 -    98.08: 3
       98.08 -   122.60: 1
  Dihedral angle restraints: 5208
    sinusoidal: 1958
      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 5205 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:             0.480
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.330
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:             0.000
  Load rotamer database and sin/cos tables:5.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
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  : 13.368 122.600   3119
  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 aren 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
  covalent geometry    : bond        0.00557 ( 8855)
  covalent geometry    : angle       0.64459 (12042)
  SS BOND              : bond        0.00644 (    1)
  SS BOND              : angle       0.69569 (    2)
  hydrogen bonds       : bond        0.13729 (  456)
  hydrogen bonds       : angle       5.74050 ( 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  : 0.201 
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: 0.7848 (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: 0.7584 (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: 0.5371
  time to fit residues: 91.6703
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  : 0.314 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  16 ASN
B  36 ASN
E  77 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 = 0.3575 r_free = 0.3575 target = 0.111026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.082654 restraints weight = 15674.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.66
r_work: 0.2992 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1140

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     :  0.587   7.480  12044  Z= 0.303
  Chirality :  0.042   0.134   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  5.365  89.389   1249
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.07 %
    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 aren not related in a simple way.
  whole:  1.32 (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   0.007   0.000   ARG E 160 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.012   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
  covalent geometry    : bond        0.00351 ( 8855)
  covalent geometry    : angle       0.58681 (12042)
  SS BOND              : bond        0.00581 (    1)
  SS BOND              : angle       0.53346 (    2)
  hydrogen bonds       : bond        0.04425 (  456)
  hydrogen bonds       : angle       4.64659 ( 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: 17
    poor density    : 130
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: B   16 ASN cc_start: 0.8686 (m-40) cc_final: 0.8278 (m110)
REVERT: B   20 ASP cc_start: 0.8270 (m-30) cc_final: 0.8006 (m-30)
REVERT: B  175 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8320 (mp10)
REVERT: B  260 GLU cc_start: 0.8492 (tt0) cc_final: 0.8261 (tt0)
REVERT: E   93 MET cc_start: 0.8657 (tpt) cc_final: 0.8141 (tpt)
REVERT: E  201 ASP cc_start: 0.8562 (p0) cc_final: 0.7953 (t70)
REVERT: R   53 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8728 (tp)
REVERT: R  137 HIS cc_start: 0.8183 (t-90) cc_final: 0.7729 (t-90)
REVERT: R  161 ASN cc_start: 0.8363 (t0) cc_final: 0.8078 (t0)
REVERT: R  170 CYS cc_start: 0.8031 (m) cc_final: 0.7715 (m)
REVERT: R  221 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6696 (ttm170)
REVERT: R  240 TYR cc_start: 0.8712 (t80) cc_final: 0.8323 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 139
  average time/residue: 0.4792
  time to fit residues: 71.1381
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  : 0.337 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
B  36 ASN
C  11 GLN
E  77 ASN
R  23 ASN
R  47 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 = 0.3582 r_free = 0.3582 target = 0.111616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083449 restraints weight = 15525.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.64
r_work: 0.3003 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8856  Z= 0.135
  Angle     :  0.550   7.185  12044  Z= 0.284
  Chirality :  0.041   0.130   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  5.125  75.392   1249
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.73 %
    Favored  : 82.50 %
  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 aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1118
  helix:  2.33 (0.26), residues: 378
  sheet:  0.71 (0.33), residues: 274
  loop : -0.15 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   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 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8855)
  covalent geometry    : angle       0.54982 (12042)
  SS BOND              : bond        0.00544 (    1)
  SS BOND              : angle       0.47216 (    2)
  hydrogen bonds       : bond        0.04053 (  456)
  hydrogen bonds       : angle       4.40793 ( 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
  165 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8260 (m-30) cc_final: 0.8053 (m-30)
REVERT: B  175 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8373 (mp10)
REVERT: B  254 ASP cc_start: 0.8665 (t0) cc_final: 0.8435 (t0)
REVERT: E   19 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8789 (tttm)
REVERT: E   51 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8748 (tp)
REVERT: E   93 MET cc_start: 0.8588 (tpt) cc_final: 0.8383 (tpt)
REVERT: E  109 ASP cc_start: 0.8650 (p0) cc_final: 0.8349 (p0)
REVERT: E  118 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6649 (m)
REVERT: E  201 ASP cc_start: 0.8566 (p0) cc_final: 0.7933 (t70)
REVERT: R   52 ASP cc_start: 0.8747 (t70) cc_final: 0.8499 (t70)
REVERT: R   53 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8745 (tp)
REVERT: R  137 HIS cc_start: 0.8162 (t-90) cc_final: 0.7785 (t-90)
REVERT: R  161 ASN cc_start: 0.8150 (t0) cc_final: 0.7829 (t0)
REVERT: R  170 CYS cc_start: 0.7926 (m) cc_final: 0.7644 (m)
REVERT: R  221 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6908 (tpt170)
REVERT: R  240 TYR cc_start: 0.8717 (t80) cc_final: 0.8324 (t80)
  outliers start: 34
  outliers final: 10
  residues processed: 146
  average time/residue: 0.5263
  time to fit residues: 81.6792
Evaluate side-chains
  130 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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 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   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  269 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0030
   chunk 105 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   overall best weight:    2.3396

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
B  35 ASN
B  36 ASN
B  75 GLN
C  44 HIS
R 115 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.109733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.081441 restraints weight = 15868.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.65
r_work: 0.2969 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8856  Z= 0.184
  Angle     :  0.588  10.132  12044  Z= 0.301
  Chirality :  0.043   0.133   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.211  66.711   1249
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.83 %
    Favored  : 79.51 %
  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 aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1118
  helix:  2.18 (0.26), residues: 384
  sheet:  0.63 (0.32), residues: 288
  loop : -0.16 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   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   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8855)
  covalent geometry    : angle       0.58826 (12042)
  SS BOND              : bond        0.00520 (    1)
  SS BOND              : angle       0.54883 (    2)
  hydrogen bonds       : bond        0.04379 (  456)
  hydrogen bonds       : angle       4.48963 ( 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
  157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7588 (mt-10)
REVERT: B   20 ASP cc_start: 0.8236 (m-30) cc_final: 0.8017 (m-30)
REVERT: B  175 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8310 (mp10)
REVERT: B  217 MET cc_start: 0.8104 (pp-130) cc_final: 0.7569 (pp-130)
REVERT: B  254 ASP cc_start: 0.8799 (t0) cc_final: 0.8587 (t0)
REVERT: E   19 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8778 (tttm)
REVERT: E   51 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8801 (tp)
REVERT: E  160 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8192 (ttm110)
REVERT: R   53 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8758 (tp)
REVERT: R  137 HIS cc_start: 0.8173 (t-90) cc_final: 0.7787 (t-90)
REVERT: R  161 ASN cc_start: 0.8303 (t0) cc_final: 0.7906 (t0)
REVERT: R  170 CYS cc_start: 0.7985 (m) cc_final: 0.7697 (m)
REVERT: R  221 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6728 (ttm170)
  outliers start: 33
  outliers final: 14
  residues processed: 140
  average time/residue: 0.4834
  time to fit residues: 72.1051
Evaluate side-chains
  139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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 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   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:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 66 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 GLN
A 229 GLN
B  35 ASN
E  77 ASN
R  23 ASN
R  47 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 = 0.3557 r_free = 0.3557 target = 0.109889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.081500 restraints weight = 15871.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.65
r_work: 0.2972 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8856  Z= 0.175
  Angle     :  0.584   9.633  12044  Z= 0.301
  Chirality :  0.042   0.135   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.196  59.474   1249
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.83 %
    Favored  : 78.18 %
  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 aren not related in a simple way.
  whole:  1.22 (0.26), residues: 1118
  helix:  2.17 (0.26), residues: 384
  sheet:  0.68 (0.33), residues: 280
  loop : -0.24 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 160 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.024   0.002   TRP R 131 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8855)
  covalent geometry    : angle       0.58385 (12042)
  SS BOND              : bond        0.00532 (    1)
  SS BOND              : angle       0.47130 (    2)
  hydrogen bonds       : bond        0.04313 (  456)
  hydrogen bonds       : angle       4.45417 ( 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
  162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8255 (m-30) cc_final: 0.7964 (m-30)
REVERT: B  254 ASP cc_start: 0.8794 (t0) cc_final: 0.8577 (t0)
REVERT: E   19 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8785 (tttm)
REVERT: E   51 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8798 (tp)
REVERT: E  109 ASP cc_start: 0.8654 (p0) cc_final: 0.8374 (p0)
REVERT: R   23 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8695 (t0)
REVERT: R   52 ASP cc_start: 0.8772 (t70) cc_final: 0.8453 (t70)
REVERT: R   53 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8796 (tp)
REVERT: R  161 ASN cc_start: 0.8222 (t0) cc_final: 0.7862 (t0)
REVERT: R  170 CYS cc_start: 0.8010 (m) cc_final: 0.7767 (m)
REVERT: R  240 TYR cc_start: 0.8691 (t80) cc_final: 0.8381 (t80)
  outliers start: 36
  outliers final: 17
  residues processed: 143
  average time/residue: 0.5089
  time to fit residues: 77.5612
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  : 0.321 
-------------------------------------------------------------------------------
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   19 ARG
Chi-restraints excluded: chain B residue  262 MET
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   83 MET
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  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:    0.3980
   chunk 107 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 229 GLN
B  35 ASN
B  75 GLN
B 110 ASN
E  77 ASN
R  23 ASN
R 115 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.111964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.083783 restraints weight = 15670.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.65
r_work: 0.3014 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1746

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= 0.120
  Angle     :  0.562   9.093  12044  Z= 0.285
  Chirality :  0.041   0.137   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.965  64.451   1249
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.16 %
    Favored  : 77.08 %
  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 aren not related in a simple way.
  whole:  1.33 (0.26), residues: 1118
  helix:  2.24 (0.26), residues: 384
  sheet:  0.77 (0.32), residues: 281
  loop : -0.20 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 160 
 TYR   0.012   0.001   TYR A 204 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.026   0.002   TRP R 131 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8855)
  covalent geometry    : angle       0.56189 (12042)
  SS BOND              : bond        0.00488 (    1)
  SS BOND              : angle       0.39123 (    2)
  hydrogen bonds       : bond        0.03817 (  456)
  hydrogen bonds       : angle       4.28023 ( 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
  161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7591 (mt-10)
REVERT: A  167 ASP cc_start: 0.8085 (t70) cc_final: 0.7694 (p0)
REVERT: B   19 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7784 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8277 (m-30) cc_final: 0.7986 (m-30)
REVERT: B  254 ASP cc_start: 0.8741 (t0) cc_final: 0.8514 (t0)
REVERT: E   19 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8790 (tttm)
REVERT: E   51 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8754 (tp)
REVERT: E  109 ASP cc_start: 0.8702 (p0) cc_final: 0.8408 (p0)
REVERT: E  160 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8236 (ttm110)
REVERT: R   23 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8642 (t0)
REVERT: R   52 ASP cc_start: 0.8842 (t70) cc_final: 0.8506 (t70)
REVERT: R   53 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8766 (tp)
REVERT: R  137 HIS cc_start: 0.8039 (t70) cc_final: 0.7607 (t-90)
REVERT: R  161 ASN cc_start: 0.8232 (t0) cc_final: 0.7876 (t0)
REVERT: R  170 CYS cc_start: 0.7721 (m) cc_final: 0.7462 (m)
REVERT: R  240 TYR cc_start: 0.8677 (t80) cc_final: 0.8340 (t80)
  outliers start: 34
  outliers final: 10
  residues processed: 146
  average time/residue: 0.4571
  time to fit residues: 71.0665
Evaluate side-chains
  135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   83 MET
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   53 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   78 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:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
B  35 ASN
B 220 GLN
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 = 0.3584 r_free = 0.3584 target = 0.111829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.083682 restraints weight = 15831.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.65
r_work: 0.3007 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8856  Z= 0.129
  Angle     :  0.576   8.551  12044  Z= 0.291
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.954  67.103   1249
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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 aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1118
  helix:  2.29 (0.26), residues: 380
  sheet:  0.70 (0.32), residues: 289
  loop : -0.15 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 214 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.023   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8855)
  covalent geometry    : angle       0.57557 (12042)
  SS BOND              : bond        0.00472 (    1)
  SS BOND              : angle       0.42601 (    2)
  hydrogen bonds       : bond        0.03841 (  456)
  hydrogen bonds       : angle       4.25114 ( 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
  156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7550 (mt-10)
REVERT: B   19 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8280 (m-30) cc_final: 0.8002 (m-30)
REVERT: B  254 ASP cc_start: 0.8745 (t0) cc_final: 0.8519 (t0)
REVERT: E   19 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8788 (tttm)
REVERT: E   51 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8767 (tp)
REVERT: E  109 ASP cc_start: 0.8666 (p0) cc_final: 0.8381 (p0)
REVERT: E  160 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8253 (ttm110)
REVERT: R   23 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8583 (t0)
REVERT: R   52 ASP cc_start: 0.8814 (t70) cc_final: 0.8479 (t70)
REVERT: R   53 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8779 (tp)
REVERT: R  137 HIS cc_start: 0.8153 (t70) cc_final: 0.7653 (t-90)
REVERT: R  161 ASN cc_start: 0.8230 (t0) cc_final: 0.7868 (t0)
REVERT: R  170 CYS cc_start: 0.7773 (m) cc_final: 0.7517 (m)
  outliers start: 30
  outliers final: 13
  residues processed: 139
  average time/residue: 0.5868
  time to fit residues: 86.4571
Evaluate side-chains
  140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
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   19 ARG
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   83 MET
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   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:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 95 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  67 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.111236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.083137 restraints weight = 15702.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.63
r_work: 0.3001 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8856  Z= 0.143
  Angle     :  0.583   8.591  12044  Z= 0.296
  Chirality :  0.041   0.136   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.992  68.832   1249
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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 aren not related in a simple way.
  whole:  1.28 (0.26), residues: 1118
  helix:  2.19 (0.26), residues: 386
  sheet:  0.64 (0.32), residues: 287
  loop : -0.16 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 214 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.023   0.002   TRP R 131 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8855)
  covalent geometry    : angle       0.58331 (12042)
  SS BOND              : bond        0.00487 (    1)
  SS BOND              : angle       0.41654 (    2)
  hydrogen bonds       : bond        0.03937 (  456)
  hydrogen bonds       : angle       4.26783 ( 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: 30
    poor density    : 124
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7553 (mt-10)
REVERT: B   19 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7780 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8291 (m-30) cc_final: 0.8017 (m-30)
REVERT: B  254 ASP cc_start: 0.8740 (t0) cc_final: 0.8514 (t0)
REVERT: E   19 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8796 (tttm)
REVERT: E   51 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8781 (tp)
REVERT: E   93 MET cc_start: 0.8613 (tpt) cc_final: 0.8398 (tpt)
REVERT: E  109 ASP cc_start: 0.8644 (p0) cc_final: 0.8376 (p0)
REVERT: E  160 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8206 (ttm110)
REVERT: R   23 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8651 (t0)
REVERT: R   52 ASP cc_start: 0.8817 (t70) cc_final: 0.8487 (t70)
REVERT: R   53 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8779 (tp)
REVERT: R  137 HIS cc_start: 0.8116 (t70) cc_final: 0.7658 (t-90)
REVERT: R  161 ASN cc_start: 0.8283 (t0) cc_final: 0.7911 (t0)
  outliers start: 30
  outliers final: 18
  residues processed: 138
  average time/residue: 0.4819
  time to fit residues: 71.0836
Evaluate side-chains
  143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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   61 ILE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  100 VAL
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   83 MET
Chi-restraints excluded: chain E residue  159 CYS
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  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:    0.6980
   chunk 94 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 229 GLN
B  35 ASN
E  77 ASN
R  23 ASN
R  47 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 = 0.3604 r_free = 0.3604 target = 0.113304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.085305 restraints weight = 15640.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.64
r_work: 0.3038 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8856  Z= 0.110
  Angle     :  0.571   8.963  12044  Z= 0.288
  Chirality :  0.041   0.138   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.843  70.454   1249
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.04 %
    Favored  : 76.08 %
  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 aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1118
  helix:  2.26 (0.26), residues: 380
  sheet:  0.73 (0.33), residues: 284
  loop : -0.16 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 160 
 TYR   0.011   0.001   TYR A 204 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.023   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8855)
  covalent geometry    : angle       0.57124 (12042)
  SS BOND              : bond        0.00474 (    1)
  SS BOND              : angle       0.35056 (    2)
  hydrogen bonds       : bond        0.03591 (  456)
  hydrogen bonds       : angle       4.17593 ( 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
  155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7736 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8220 (m-30) cc_final: 0.7880 (m-30)
REVERT: B  254 ASP cc_start: 0.8778 (t0) cc_final: 0.8545 (t0)
REVERT: E   51 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8727 (tp)
REVERT: E   93 MET cc_start: 0.8606 (tpt) cc_final: 0.8390 (tpt)
REVERT: E  109 ASP cc_start: 0.8677 (p0) cc_final: 0.8421 (p0)
REVERT: E  160 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8182 (ttm110)
REVERT: E  220 GLU cc_start: 0.7583 (mp0) cc_final: 0.6992 (mp0)
REVERT: R   23 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8602 (t0)
REVERT: R   52 ASP cc_start: 0.8805 (t70) cc_final: 0.8475 (t70)
REVERT: R   53 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8758 (tp)
REVERT: R  137 HIS cc_start: 0.8124 (t70) cc_final: 0.7672 (t-90)
REVERT: R  161 ASN cc_start: 0.8289 (t0) cc_final: 0.7954 (t0)
REVERT: R  170 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7050 (m)
REVERT: R  190 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8912 (mp)
  outliers start: 26
  outliers final: 10
  residues processed: 142
  average time/residue: 0.4656
  time to fit residues: 70.6294
Evaluate side-chains
  142 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  318 LEU
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  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 104 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 108 optimal weight:    6.9990
   chunk 96 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0470
   chunk 62 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.9684

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
B  35 ASN
R  23 ASN
** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.110632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082557 restraints weight = 15776.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.64
r_work: 0.2990 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8856  Z= 0.166
  Angle     :  0.612   9.574  12044  Z= 0.310
  Chirality :  0.042   0.134   1356
  Planarity :  0.004   0.050   1543
  Dihedral  :  5.043  72.153   1249
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.37 %
    Favored  : 76.08 %
  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 aren not related in a simple way.
  whole:  1.24 (0.26), residues: 1118
  helix:  2.15 (0.26), residues: 386
  sheet:  0.63 (0.32), residues: 288
  loop : -0.17 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 180 
 TRP   0.022   0.002   TRP R 131 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8855)
  covalent geometry    : angle       0.61185 (12042)
  SS BOND              : bond        0.00481 (    1)
  SS BOND              : angle       0.44423 (    2)
  hydrogen bonds       : bond        0.04109 (  456)
  hydrogen bonds       : angle       4.31505 ( 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: 23
    poor density    : 127
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7772 (ttp-110)
REVERT: B   20 ASP cc_start: 0.8163 (m-30) cc_final: 0.7843 (m-30)
REVERT: B  254 ASP cc_start: 0.8735 (t0) cc_final: 0.8491 (t0)
REVERT: E   19 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8817 (tttm)
REVERT: E   51 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8765 (tp)
REVERT: E  109 ASP cc_start: 0.8666 (p0) cc_final: 0.8407 (p0)
REVERT: R   52 ASP cc_start: 0.8760 (t70) cc_final: 0.8386 (t70)
REVERT: R   53 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8736 (tp)
REVERT: R  137 HIS cc_start: 0.7971 (t70) cc_final: 0.7535 (t-90)
REVERT: R  161 ASN cc_start: 0.8364 (t0) cc_final: 0.7924 (t0)
REVERT: R  170 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7240 (m)
REVERT: R  190 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8997 (mp)
  outliers start: 23
  outliers final: 12
  residues processed: 138
  average time/residue: 0.4953
  time to fit residues: 73.0607
Evaluate side-chains
  140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  172 THR
Chi-restraints excluded: chain E residue  186 GLN
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:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 98 optimal weight:    0.2980
   chunk 101 optimal weight:    3.9990
   chunk 92 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 229 GLN
B  35 ASN
E  77 ASN
R  23 ASN
R  86 HIS
** 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 = 0.3597 r_free = 0.3597 target = 0.112793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.084730 restraints weight = 15627.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.64
r_work: 0.3027 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1994

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= 0.122
  Angle     :  0.611  10.507  12044  Z= 0.306
  Chirality :  0.041   0.138   1356
  Planarity :  0.004   0.051   1543
  Dihedral  :  4.919  72.802   1249
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.82 %
    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 aren not related in a simple way.
  whole:  1.36 (0.26), residues: 1118
  helix:  2.34 (0.27), residues: 372
  sheet:  0.73 (0.33), residues: 284
  loop : -0.14 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 160 
 TYR   0.013   0.001   TYR A 204 
 PHE   0.012   0.001   PHE R  87 
 TRP   0.024   0.001   TRP R 131 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8855)
  covalent geometry    : angle       0.61080 (12042)
  SS BOND              : bond        0.00467 (    1)
  SS BOND              : angle       0.36120 (    2)
  hydrogen bonds       : bond        0.03722 (  456)
  hydrogen bonds       : angle       4.22819 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2892.70 seconds
wall clock time: 49 minutes 58.70 seconds (2998.70 seconds total)