Starting phenix.real_space_refine
on Sat Aug 23 03:02:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8blq_16113/08_2025/8blq_16113.cif"
  }
  resolution = 3.97
  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=   0.012
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      38      5.16       5
     C    5787      2.51       5
     N    1550      2.21       5
     O    1835      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  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: 9210
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2597
          Classifications: {'peptide': 343}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 16, 'TRANS': 322}
    Chain: "B"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2514
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 5, 'PTRANS': 11, 'TRANS': 317}
    Chain: "C"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1584
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "E"
      Number of atoms: 1671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1671
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210}
  Time building chain proxies: 1.97, per 1000 atoms: 0.21
  Number of scatterers: 9210
  At special positions: 0
  Unit cell: (167.881, 118.261, 87.662, 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      38     16.00
     O    1835      8.00
     N    1550      7.00
     C    5787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 257 " - pdb=" SG  CYS B 317 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 136 " - pdb=" SG  CYS C 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 322.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2214

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 30 sheets defined
      11.8% alpha, 28.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.628A  pdb=" N   SER A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 156
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'B' and resid 197 through 201
      removed outlier: 3.560A  pdb=" N   ILE B 201 " --> pdb=" O   PRO B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 249
    Processing helix  chain 'B' and resid 306 through 311
      removed outlier: 3.680A  pdb=" N   LYS B 311 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 82
    Processing helix  chain 'C' and resid 123 through 129
    Processing helix  chain 'C' and resid 183 through 190
      removed outlier: 3.576A  pdb=" N   HIS C 190 " --> pdb=" O   GLN C 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 39
      removed outlier: 4.253A  pdb=" N   LEU D  28 " --> pdb=" O   PRO D  24 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG D  29 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 50
      removed outlier: 4.160A  pdb=" N   GLY D  49 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER D  50 " --> pdb=" O   CYS D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 70
    Processing helix  chain 'D' and resid 78 through 89
    Processing helix  chain 'D' and resid 94 through 98
      removed outlier: 3.713A  pdb=" N   GLN D  97 " --> pdb=" O   SER D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 105
      removed outlier: 3.622A  pdb=" N   VAL D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 127
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 194 through 198
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.501A  pdb=" N   SER A  25 " --> pdb=" O   GLN A   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.782A  pdb=" N   ILE A  37 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102
      removed outlier: 3.777A  pdb=" N   LYS A 100 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131
      removed outlier: 3.559A  pdb=" N   GLN A 127 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182
      removed outlier: 5.352A  pdb=" N   TRP A 171 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ARG A 162 " --> pdb=" O   TRP A 171 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY A 173 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182
      removed outlier: 5.352A  pdb=" N   TRP A 171 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ARG A 162 " --> pdb=" O   TRP A 171 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY A 173 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ARG A 221 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 192
      removed outlier: 3.739A  pdb=" N   SER A 192 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 253 through 255
    Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 268
      removed outlier: 6.537A  pdb=" N   SER A 311 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA A 299 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL A 313 " --> pdb=" O   PHE A 297 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 285
    Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.563A  pdb=" N   SER B  22 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR B  76 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER B  69 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 31
    Processing sheet with id=AB5, first strand: chain 'B' and resid 57 through 58
      removed outlier: 3.586A  pdb=" N   LEU B  51 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TRP B  39 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   TYR B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   MET B  37 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 58
      removed outlier: 3.586A  pdb=" N   LEU B  51 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TRP B  39 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   TYR B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   MET B  37 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLN B  94 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR B 101 " --> pdb=" O   GLN B  94 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 140 through 142
    Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 172
      removed outlier: 6.805A  pdb=" N   TRP B 153 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 240
      removed outlier: 4.191A  pdb=" N   SER B 254 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU B 304 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   VAL B 256 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU B 302 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   LEU B 258 " --> pdb=" O   SER B 300 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   SER B 300 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASN B 260 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   LEU B 298 " --> pdb=" O   ASN B 260 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B 285 " --> pdb=" O   SER B 299 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 267 through 269
    Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 273
      removed outlier: 4.439A  pdb=" N   TYR B 315 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   PHE B 332 " --> pdb=" O   TYR B 315 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   CYS B 317 " --> pdb=" O   LYS B 330 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LYS B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 12
      removed outlier: 6.586A  pdb=" N   VAL C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN C  88 " --> pdb=" O   HIS C  33 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 9 through 12
      removed outlier: 6.586A  pdb=" N   VAL C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL C  89 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL C  98 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 18 through 22
      removed outlier: 4.096A  pdb=" N   ALA C  70 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 120
      removed outlier: 3.548A  pdb=" N   VAL C 135 " --> pdb=" O   PHE C 120 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA C 132 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   TYR C 174 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 155 through 156
      removed outlier: 3.698A  pdb=" N   CYS C 195 " --> pdb=" O   LYS C 206 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS C 206 " --> pdb=" O   CYS C 195 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 52 through 53
    Processing sheet with id=AC9, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.766A  pdb=" N   VAL E 118 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA E  92 " --> pdb=" O   VAL E 118 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 129 through 132
      removed outlier: 3.583A  pdb=" N   PHE E 131 " --> pdb=" O   LEU E 150 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER E 189 " --> pdb=" O   CYS E 149 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP E 153 " --> pdb=" O   TYR E 185 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TYR E 185 " --> pdb=" O   ASP E 153 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 159 through 163
      removed outlier: 3.525A  pdb=" N   VAL E 207 " --> pdb=" O   VAL E 216 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL E 216 " --> pdb=" O   VAL E 207 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    609 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: 1.05

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2973
        1.34 -     1.46: 2242
        1.46 -     1.58: 4161
        1.58 -     1.70: 0
        1.70 -     1.81: 51
  Bond restraints: 9427
  Sorted by residual:
  bond pdb=" N   ILE C  26 "
       pdb=" CA  ILE C  26 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.19e+00
  bond pdb=" N   ASN C  25 "
       pdb=" CA  ASN C  25 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.13e+00
  bond pdb=" N   ILE C  27 "
       pdb=" CA  ILE C  27 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.28e-02 6.10e+03 5.46e+00
  bond pdb=" C   LYS E 210 "
       pdb=" N   PRO E 211 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.30e-02 5.92e+03 1.51e+00
  bond pdb=" CG  PRO B 264 "
       pdb=" CD  PRO B 264 "
    ideal  model  delta    sigma   weight residual
    1.512  1.483  0.029 2.70e-02 1.37e+03 1.13e+00
  ... (remaining 9422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 12465
        1.40 -     2.80: 320
        2.80 -     4.20: 37
        4.20 -     5.61: 2
        5.61 -     7.01: 6
  Bond angle restraints: 12830
  Sorted by residual:
  angle pdb=" N   ILE C  27 "
        pdb=" CA  ILE C  27 "
        pdb=" C   ILE C  27 "
      ideal   model   delta    sigma   weight residual
     113.16  106.50    6.66 1.49e+00 4.50e-01 2.00e+01
  angle pdb=" C   ILE B 147 "
        pdb=" N   ASP B 148 "
        pdb=" CA  ASP B 148 "
      ideal   model   delta    sigma   weight residual
     121.54  128.55   -7.01 1.91e+00 2.74e-01 1.35e+01
  angle pdb=" N   ILE B 147 "
        pdb=" CA  ILE B 147 "
        pdb=" C   ILE B 147 "
      ideal   model   delta    sigma   weight residual
     111.62  108.83    2.79 7.90e-01 1.60e+00 1.25e+01
  angle pdb=" C   GLY D  74 "
        pdb=" N   CYS D  75 "
        pdb=" CA  CYS D  75 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  angle pdb=" N   THR C  69 "
        pdb=" CA  THR C  69 "
        pdb=" C   THR C  69 "
      ideal   model   delta    sigma   weight residual
     107.93  111.74   -3.81 1.65e+00 3.67e-01 5.32e+00
  ... (remaining 12825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 5162
       17.84 -    35.68: 367
       35.68 -    53.52: 57
       53.52 -    71.37: 9
       71.37 -    89.21: 3
  Dihedral angle restraints: 5598
    sinusoidal: 2120
      harmonic: 3478
  Sorted by residual:
  dihedral pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  96 "
           pdb=" CB  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.69  -51.69     1      1.00e+01 1.00e-02 3.65e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  87 "
           pdb=" CB  CYS C  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.53   46.47     1      1.00e+01 1.00e-02 2.99e+01
  dihedral pdb=" CA  SER B  71 "
           pdb=" C   SER B  71 "
           pdb=" N   ARG B  72 "
           pdb=" CA  ARG B  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 5595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1016
       0.037 -    0.074: 287
       0.074 -    0.111: 118
       0.111 -    0.148: 15
       0.148 -    0.185: 2
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" CA  ILE C  27 "
            pdb=" N   ILE C  27 "
            pdb=" C   ILE C  27 "
            pdb=" CB  ILE C  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CA  ILE C  26 "
            pdb=" N   ILE C  26 "
            pdb=" C   ILE C  26 "
            pdb=" CB  ILE C  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.19e-01
  chirality pdb=" CB  ILE B 137 "
            pdb=" CA  ILE B 137 "
            pdb=" CG1 ILE B 137 "
            pdb=" CG2 ILE B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1435 not shown)

  Planarity restraints: 1649
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 279 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A 280 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  24 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.90e+00
        pdb=" C   GLY C  24 "    0.024 2.00e-02 2.50e+03
        pdb=" O   GLY C  24 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN C  25 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 183 "    0.022 5.00e-02 4.00e+02   3.30e-02 1.75e+00
        pdb=" N   PRO C 184 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1646 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 794
        2.74 -     3.28: 9273
        3.28 -     3.82: 15357
        3.82 -     4.36: 17650
        4.36 -     4.90: 30315
  Nonbonded interactions: 73389
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 186 "
            pdb=" OH  TYR C 193 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OE1 GLN B   6 "
            pdb=" OG1 THR B 106 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   HIS C 199 "
            pdb=" OG  SER C 202 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER C 194 "
            pdb=" O   LYS C 206 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER E  52 "
            pdb=" OD1 ASN E  55 "
     model   vdw
     2.234 3.040
  ... (remaining 73384 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.950
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
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      :  0.002   0.034   9434  Z= 0.129
  Angle     :  0.551   7.007  12844  Z= 0.320
  Chirality :  0.041   0.185   1438
  Planarity :  0.004   0.037   1649
  Dihedral  : 12.200  89.206   3363
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.51 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -3.81 (0.22), residues: 1210
  helix: -1.23 (0.49), residues: 91
  sheet: -2.75 (0.22), residues: 412
  loop : -2.61 (0.21), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  72 
 TYR   0.006   0.001   TYR A 218 
 PHE   0.009   0.001   PHE B 189 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.002   0.000   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 9427)
  covalent geometry    : angle       0.55083 (12830)
  SS BOND              : bond        0.00228 (    7)
  SS BOND              : angle       0.70044 (   14)
  hydrogen bonds       : bond        0.26380 (  262)
  hydrogen bonds       : angle      11.19555 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1123
  time to fit residues: 9.0376
Evaluate side-chains
  26 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 286 ASN
A 335 ASN
B   6 GLN
B  17 GLN
B  83 GLN
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
C   6 GLN
C  36 GLN
C 128 GLN
** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
E   6 GLN
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.034609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.024959 restraints weight = 165968.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.025610 restraints weight = 109209.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.026079 restraints weight = 80816.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.026405 restraints weight = 64826.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.026650 restraints weight = 54889.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   9434  Z= 0.228
  Angle     :  0.639   7.958  12844  Z= 0.332
  Chirality :  0.042   0.121   1438
  Planarity :  0.005   0.053   1649
  Dihedral  :  4.914  89.893   1305
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  8.58 %
    Favored  : 89.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -3.08 (0.23), residues: 1210
  helix: -0.72 (0.55), residues: 92
  sheet: -2.44 (0.24), residues: 405
  loop : -1.99 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 191 
 TYR   0.017   0.002   TYR E 203 
 PHE   0.016   0.002   PHE B  75 
 TRP   0.038   0.002   TRP A 285 
 HIS   0.007   0.002   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 9427)
  covalent geometry    : angle       0.63893 (12830)
  SS BOND              : bond        0.00286 (    7)
  SS BOND              : angle       1.00628 (   14)
  hydrogen bonds       : bond        0.04625 (  262)
  hydrogen bonds       : angle       7.76550 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8800 (mp10)
REVERT: A   74 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5095 (mm-30)
REVERT: D   61 MET cc_start: 0.9301 (pmm) cc_final: 0.8866 (pmm)
REVERT: D  102 HIS cc_start: 0.9323 (p-80) cc_final: 0.9090 (p-80)
  outliers start: 15
  outliers final: 7
  residues processed: 40
  average time/residue: 0.1006
  time to fit residues: 5.8543
Evaluate side-chains
  27 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain E residue  193 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 114 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN
A  65 GLN
A 323 GLN
B  41 GLN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.032992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.024991 restraints weight = 173238.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.025604 restraints weight = 109601.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.026044 restraints weight = 78605.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.026375 restraints weight = 61590.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.026611 restraints weight = 50901.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106   9434  Z= 0.342
  Angle     :  0.762  13.581  12844  Z= 0.393
  Chirality :  0.045   0.167   1438
  Planarity :  0.005   0.053   1649
  Dihedral  :  5.733  87.660   1305
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 26.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.87 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.91 (0.23), residues: 1210
  helix: -1.43 (0.48), residues: 99
  sheet: -2.29 (0.24), residues: 398
  loop : -1.77 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 334 
 TYR   0.016   0.002   TYR C 179 
 PHE   0.019   0.003   PHE B  75 
 TRP   0.022   0.003   TRP B 271 
 HIS   0.008   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00702 ( 9427)
  covalent geometry    : angle       0.76198 (12830)
  SS BOND              : bond        0.00408 (    7)
  SS BOND              : angle       1.03462 (   14)
  hydrogen bonds       : bond        0.04489 (  262)
  hydrogen bonds       : angle       7.68540 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 21
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5619 (mm-30)
REVERT: A  174 MET cc_start: 0.8697 (ptm) cc_final: 0.8365 (ppp)
REVERT: A  229 MET cc_start: 0.9123 (mtm) cc_final: 0.8286 (mtm)
REVERT: D   61 MET cc_start: 0.9402 (pmm) cc_final: 0.8346 (pmm)
REVERT: D   84 MET cc_start: 0.9686 (mtm) cc_final: 0.9051 (mtm)
  outliers start: 16
  outliers final: 11
  residues processed: 36
  average time/residue: 0.0774
  time to fit residues: 4.4112
Evaluate side-chains
  31 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 19
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  193 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 295 HIS
B 260 ASN
B 261 ASN
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 196 GLN
D  40 GLN
** E 164 ASN ** 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 = 0.3370 r_free = 0.3370 target = 0.033578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.024204 restraints weight = 169354.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.024915 restraints weight = 104241.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.025367 restraints weight = 74096.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.025740 restraints weight = 58166.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.025989 restraints weight = 48428.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9434  Z= 0.130
  Angle     :  0.557   9.305  12844  Z= 0.284
  Chirality :  0.043   0.139   1438
  Planarity :  0.004   0.037   1649
  Dihedral  :  5.158  80.184   1305
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.62 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.49 (0.24), residues: 1210
  helix: -0.82 (0.52), residues: 100
  sheet: -1.99 (0.25), residues: 376
  loop : -1.58 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 106 
 TYR   0.013   0.001   TYR A 307 
 PHE   0.012   0.001   PHE B  75 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9427)
  covalent geometry    : angle       0.55682 (12830)
  SS BOND              : bond        0.00203 (    7)
  SS BOND              : angle       0.66767 (   14)
  hydrogen bonds       : bond        0.03030 (  262)
  hydrogen bonds       : angle       6.68245 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 19
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  343 GLU cc_start: 0.8724 (tp30) cc_final: 0.8270 (tm-30)
REVERT: B   37 MET cc_start: 0.7515 (tmm) cc_final: 0.6464 (tmm)
REVERT: D   61 MET cc_start: 0.9470 (pmm) cc_final: 0.8343 (pmm)
REVERT: D   84 MET cc_start: 0.9628 (mtm) cc_final: 0.9197 (mtm)
  outliers start: 15
  outliers final: 8
  residues processed: 32
  average time/residue: 0.0886
  time to fit residues: 4.4280
Evaluate side-chains
  25 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain E residue   30 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 110 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.032475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.024633 restraints weight = 172243.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.025259 restraints weight = 105329.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.025708 restraints weight = 74378.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.026037 restraints weight = 57818.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.026271 restraints weight = 47468.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.104   9434  Z= 0.329
  Angle     :  0.731  11.716  12844  Z= 0.373
  Chirality :  0.043   0.145   1438
  Planarity :  0.005   0.095   1649
  Dihedral  :  5.861  78.946   1305
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 27.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.72 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.62 (0.24), residues: 1210
  helix: -0.93 (0.51), residues: 98
  sheet: -2.11 (0.24), residues: 421
  loop : -1.57 (0.24), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 334 
 TYR   0.016   0.002   TYR C 179 
 PHE   0.019   0.002   PHE B  75 
 TRP   0.014   0.002   TRP A  36 
 HIS   0.008   0.002   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 ( 9427)
  covalent geometry    : angle       0.73081 (12830)
  SS BOND              : bond        0.00431 (    7)
  SS BOND              : angle       0.94739 (   14)
  hydrogen bonds       : bond        0.04010 (  262)
  hydrogen bonds       : angle       7.33336 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 19
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  343 GLU cc_start: 0.8946 (tp30) cc_final: 0.8684 (tm-30)
REVERT: D   61 MET cc_start: 0.9508 (pmm) cc_final: 0.8355 (pmm)
REVERT: E   48 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (mmm)
REVERT: E   70 MET cc_start: 0.7791 (tpt) cc_final: 0.7564 (ttm)
  outliers start: 31
  outliers final: 18
  residues processed: 46
  average time/residue: 0.0545
  time to fit residues: 4.3284
Evaluate side-chains
  38 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 19
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   48 MET
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 54 optimal weight:   30.0000
   chunk 39 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 68 optimal weight:   30.0000
   chunk 37 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 GLN
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.032685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.025094 restraints weight = 173564.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.025750 restraints weight = 104904.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.026190 restraints weight = 72209.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.026534 restraints weight = 55146.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.026758 restraints weight = 45028.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9434  Z= 0.130
  Angle     :  0.570   8.413  12844  Z= 0.289
  Chirality :  0.043   0.178   1438
  Planarity :  0.004   0.036   1649
  Dihedral  :  5.231  69.883   1305
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.08 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.31 (0.24), residues: 1210
  helix: -0.61 (0.52), residues: 99
  sheet: -1.82 (0.25), residues: 393
  loop : -1.48 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  83 
 TYR   0.008   0.001   TYR B  40 
 PHE   0.011   0.001   PHE B  75 
 TRP   0.023   0.002   TRP A  47 
 HIS   0.003   0.001   HIS B 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9427)
  covalent geometry    : angle       0.56983 (12830)
  SS BOND              : bond        0.00167 (    7)
  SS BOND              : angle       0.75484 (   14)
  hydrogen bonds       : bond        0.02839 (  262)
  hydrogen bonds       : angle       6.43386 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 19
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5747 (tm-30)
REVERT: A  174 MET cc_start: 0.8679 (ptm) cc_final: 0.8398 (ppp)
REVERT: A  229 MET cc_start: 0.8973 (mtm) cc_final: 0.7956 (mtm)
REVERT: A  343 GLU cc_start: 0.8638 (tp30) cc_final: 0.8338 (tm-30)
REVERT: B   37 MET cc_start: 0.7562 (tmm) cc_final: 0.6769 (tmm)
REVERT: D   61 MET cc_start: 0.9485 (pmm) cc_final: 0.8295 (pmm)
REVERT: D   84 MET cc_start: 0.9378 (mtp) cc_final: 0.9024 (mtm)
REVERT: E   48 MET cc_start: 0.8785 (mtt) cc_final: 0.8410 (mmm)
  outliers start: 21
  outliers final: 14
  residues processed: 38
  average time/residue: 0.0532
  time to fit residues: 3.4714
Evaluate side-chains
  34 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 19
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 110 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.032133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.024410 restraints weight = 176307.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.025008 restraints weight = 106343.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.025463 restraints weight = 75201.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.025744 restraints weight = 58019.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.026000 restraints weight = 48331.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.5812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085   9434  Z= 0.280
  Angle     :  0.677  10.310  12844  Z= 0.343
  Chirality :  0.044   0.345   1438
  Planarity :  0.005   0.041   1649
  Dihedral  :  5.723  70.721   1305
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 24.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.08 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.37 (0.24), residues: 1210
  helix: -0.76 (0.53), residues: 99
  sheet: -1.88 (0.25), residues: 411
  loop : -1.46 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  76 
 TYR   0.013   0.002   TYR C 179 
 PHE   0.016   0.002   PHE B  75 
 TRP   0.015   0.002   TRP A  47 
 HIS   0.007   0.002   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 9427)
  covalent geometry    : angle       0.67626 (12830)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       0.88991 (   14)
  hydrogen bonds       : bond        0.03599 (  262)
  hydrogen bonds       : angle       6.91803 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 18
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.6656 (OUTLIER) cc_final: 0.6264 (t60)
REVERT: A  101 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6119 (tm-30)
REVERT: B   37 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6940 (tmm)
REVERT: D   61 MET cc_start: 0.9525 (pmm) cc_final: 0.8265 (pmm)
REVERT: D   84 MET cc_start: 0.9501 (mtp) cc_final: 0.9103 (mtm)
  outliers start: 28
  outliers final: 18
  residues processed: 42
  average time/residue: 0.0685
  time to fit residues: 4.6965
Evaluate side-chains
  37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 16
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  275 ASN
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.031868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.024190 restraints weight = 174760.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.024824 restraints weight = 104750.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.025284 restraints weight = 72806.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.025582 restraints weight = 55869.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.025828 restraints weight = 46439.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.6161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   9434  Z= 0.224
  Angle     :  0.640   9.951  12844  Z= 0.326
  Chirality :  0.044   0.308   1438
  Planarity :  0.004   0.039   1649
  Dihedral  :  5.630  62.345   1305
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 21.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.37 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.33 (0.24), residues: 1210
  helix: -0.82 (0.52), residues: 99
  sheet: -1.82 (0.25), residues: 392
  loop : -1.46 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 334 
 TYR   0.012   0.002   TYR E  94 
 PHE   0.013   0.002   PHE B  75 
 TRP   0.015   0.002   TRP A  47 
 HIS   0.005   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9427)
  covalent geometry    : angle       0.64013 (12830)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       0.76154 (   14)
  hydrogen bonds       : bond        0.03262 (  262)
  hydrogen bonds       : angle       6.66925 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 17
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   50 MET cc_start: 0.0381 (pmm) cc_final: 0.0034 (pmm)
REVERT: A  101 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6078 (tm-30)
REVERT: A  174 MET cc_start: 0.8545 (ptm) cc_final: 0.8228 (ppp)
REVERT: A  181 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8744 (tp)
REVERT: D   61 MET cc_start: 0.9524 (pmm) cc_final: 0.8264 (pmm)
REVERT: D   84 MET cc_start: 0.9503 (mtp) cc_final: 0.9112 (mtm)
  outliers start: 23
  outliers final: 18
  residues processed: 38
  average time/residue: 0.0512
  time to fit residues: 3.4140
Evaluate side-chains
  36 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 16
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  207 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 112 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0270
   chunk 30 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 81 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  62 GLN
B 283 GLN
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.032238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.024857 restraints weight = 172161.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.025490 restraints weight = 101616.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.025907 restraints weight = 70023.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.026236 restraints weight = 53874.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.026486 restraints weight = 44124.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9434  Z= 0.110
  Angle     :  0.562   7.818  12844  Z= 0.285
  Chirality :  0.043   0.259   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  5.035  53.860   1305
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 17.45 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.10 (0.24), residues: 1210
  helix: -0.64 (0.52), residues: 99
  sheet: -1.54 (0.25), residues: 406
  loop : -1.38 (0.24), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 106 
 TYR   0.009   0.001   TYR B 315 
 PHE   0.010   0.001   PHE B 262 
 TRP   0.037   0.002   TRP A  47 
 HIS   0.003   0.001   HIS B 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9427)
  covalent geometry    : angle       0.56202 (12830)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       0.80335 (   14)
  hydrogen bonds       : bond        0.02622 (  262)
  hydrogen bonds       : angle       5.96748 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 20
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5615 (tm-30)
REVERT: A  174 MET cc_start: 0.8653 (ptm) cc_final: 0.8291 (ppp)
REVERT: A  343 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8513 (tm-30)
REVERT: B   37 MET cc_start: 0.7296 (tmm) cc_final: 0.6986 (tmm)
REVERT: D   61 MET cc_start: 0.9491 (pmm) cc_final: 0.8216 (pmm)
REVERT: D   84 MET cc_start: 0.9444 (mtp) cc_final: 0.9064 (mtm)
  outliers start: 15
  outliers final: 12
  residues processed: 33
  average time/residue: 0.0698
  time to fit residues: 3.7225
Evaluate side-chains
  30 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 17
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  207 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 51 optimal weight:   40.0000
   chunk 112 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   chunk 66 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 18 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    3.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.031741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.024046 restraints weight = 174332.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.024653 restraints weight = 109637.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.025067 restraints weight = 76435.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.025411 restraints weight = 58879.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.025658 restraints weight = 48289.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.6255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   9434  Z= 0.209
  Angle     :  0.626  10.519  12844  Z= 0.315
  Chirality :  0.042   0.260   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  5.250  53.794   1305
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.60 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.25 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.09 (0.24), residues: 1210
  helix: -0.69 (0.52), residues: 99
  sheet: -1.59 (0.25), residues: 396
  loop : -1.34 (0.24), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 334 
 TYR   0.010   0.001   TYR B 315 
 PHE   0.014   0.002   PHE B  75 
 TRP   0.038   0.002   TRP A  47 
 HIS   0.005   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 9427)
  covalent geometry    : angle       0.62625 (12830)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       0.68377 (   14)
  hydrogen bonds       : bond        0.03055 (  262)
  hydrogen bonds       : angle       6.28727 (  609)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 16
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  101 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5881 (tm-30)
REVERT: A  174 MET cc_start: 0.8595 (ptm) cc_final: 0.8269 (ppp)
REVERT: A  206 MET cc_start: 0.8359 (tpp) cc_final: 0.7961 (tpp)
REVERT: B   37 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6999 (tmm)
REVERT: D   61 MET cc_start: 0.9515 (pmm) cc_final: 0.8235 (pmm)
REVERT: D   84 MET cc_start: 0.9513 (mtp) cc_final: 0.9119 (mtm)
  outliers start: 18
  outliers final: 15
  residues processed: 30
  average time/residue: 0.0544
  time to fit residues: 2.9115
Evaluate side-chains
  33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 16
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   91 HIS
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue   70 MET
Chi-restraints excluded: chain E residue  172 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 112 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.031642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.024034 restraints weight = 172003.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.024643 restraints weight = 104527.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.025079 restraints weight = 73046.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.025402 restraints weight = 56522.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.025629 restraints weight = 46345.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.6916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9434  Z= 0.259
  Angle     :  0.693  10.569  12844  Z= 0.351
  Chirality :  0.044   0.281   1438
  Planarity :  0.005   0.038   1649
  Dihedral  :  5.816  54.509   1305
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 26.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.96 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    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: -2.27 (0.24), residues: 1210
  helix: -1.10 (0.49), residues: 105
  sheet: -1.57 (0.25), residues: 397
  loop : -1.51 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  83 
 TYR   0.011   0.002   TYR C 179 
 PHE   0.017   0.002   PHE B  75 
 TRP   0.038   0.002   TRP A  47 
 HIS   0.006   0.002   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 ( 9427)
  covalent geometry    : angle       0.69315 (12830)
  SS BOND              : bond        0.00298 (    7)
  SS BOND              : angle       0.86782 (   14)
  hydrogen bonds       : bond        0.03528 (  262)
  hydrogen bonds       : angle       6.81340 (  609)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1479.56 seconds
wall clock time: 26 minutes 37.06 seconds (1597.06 seconds total)