Starting phenix.real_space_refine
on Sun Jun  8 06:25:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8blq_16113/06_2025/8blq_16113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8blq_16113/06_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_16113/06_2025/8blq_16113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8blq_16113/06_2025/8blq_16113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8blq_16113/06_2025/8blq_16113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8blq_16113/06_2025/8blq_16113.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.97, per 1000 atoms: 0.65
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.53
  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: 2.74

  Time building geometry restraints manager: 2.62 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:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.800
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.220
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.005   0.001   TRP A  47 
 HIS   0.002   0.000   HIS A 295 
 PHE   0.009   0.001   PHE B 189 
 TYR   0.006   0.001   TYR A 218 
 ARG   0.001   0.000   ARG B  72 

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

*********************** 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  : 1.127 
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: 0.3259
  time to fit residues: 26.2148
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  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 50 optimal weight:   30.0000
   chunk 31 optimal weight:   30.0000
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 94 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   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 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 ASN
B   6 GLN
B  17 GLN
B  41 GLN
B  83 GLN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN
C  36 GLN
C 128 GLN
** 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   3 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.033597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.024039 restraints weight = 153121.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.024617 restraints weight = 103730.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.024893 restraints weight = 75609.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.118   9434  Z= 0.331
  Angle     :  0.776  11.030  12844  Z= 0.400
  Chirality :  0.044   0.152   1438
  Planarity :  0.005   0.061   1649
  Dihedral  :  5.465  89.757   1305
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 22.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.14 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.23), residues: 1210
  helix: -1.03 (0.52), residues: 93
  sheet: -2.58 (0.24), residues: 402
  loop : -1.94 (0.23), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 285 
 HIS   0.009   0.002   HIS C 190 
 PHE   0.022   0.003   PHE B  75 
 TYR   0.017   0.002   TYR C 193 
 ARG   0.008   0.001   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04695 (  262)
  hydrogen bonds       : angle       8.04214 (  609)
  SS BOND              : bond        0.00506 (    7)
  SS BOND              : angle       1.36982 (   14)
  covalent geometry    : bond        0.00712 ( 9427)
  covalent geometry    : angle       0.77518 (12830)

*********************** 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
  44 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8848 (mp10)
REVERT: A   74 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6339 (mm-30)
REVERT: A  285 TRP cc_start: 0.9064 (m100) cc_final: 0.8671 (m100)
REVERT: D   61 MET cc_start: 0.9442 (pmm) cc_final: 0.9014 (pmm)
REVERT: D   84 MET cc_start: 0.9689 (mtm) cc_final: 0.9001 (mtm)
  outliers start: 16
  outliers final: 7
  residues processed: 42
  average time/residue: 0.2138
  time to fit residues: 13.4571
Evaluate side-chains
  30 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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 B residue  275 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 E residue  193 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 117 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 87 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 295 HIS ** 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
E   6 GLN
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.033497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.025552 restraints weight = 171809.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.026196 restraints weight = 104861.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.026670 restraints weight = 73713.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9434  Z= 0.134
  Angle     :  0.550   8.556  12844  Z= 0.282
  Chirality :  0.043   0.156   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  5.019  86.685   1305
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 13.06 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.23), residues: 1210
  helix: -0.77 (0.53), residues: 99
  sheet: -2.20 (0.24), residues: 379
  loop : -1.77 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.025   0.002   PHE B 239 
 TYR   0.013   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  262)
  hydrogen bonds       : angle       6.96930 (  609)
  SS BOND              : bond        0.00199 (    7)
  SS BOND              : angle       0.69397 (   14)
  covalent geometry    : bond        0.00294 ( 9427)
  covalent geometry    : angle       0.54947 (12830)

*********************** 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
  29 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 MET cc_start: 0.7623 (tmm) cc_final: 0.6294 (tmm)
REVERT: D   61 MET cc_start: 0.9352 (pmm) cc_final: 0.8254 (pmm)
REVERT: D   84 MET cc_start: 0.9614 (mtm) cc_final: 0.9218 (mtm)
  outliers start: 7
  outliers final: 5
  residues processed: 28
  average time/residue: 0.2328
  time to fit residues: 10.2613
Evaluate side-chains
  24 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain D residue   91 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 79 optimal weight:   10.0000
   chunk 102 optimal weight:    7.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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  39 GLN
A  65 GLN
A 295 HIS
** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.033451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.024165 restraints weight = 168227.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.024834 restraints weight = 105280.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.025318 restraints weight = 75122.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   9434  Z= 0.235
  Angle     :  0.628  10.914  12844  Z= 0.319
  Chirality :  0.042   0.173   1438
  Planarity :  0.004   0.048   1649
  Dihedral  :  5.346  83.327   1305
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 21.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.55 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.24), residues: 1210
  helix: -0.73 (0.53), residues: 99
  sheet: -2.03 (0.26), residues: 364
  loop : -1.57 (0.23), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 271 
 HIS   0.005   0.001   HIS D 102 
 PHE   0.015   0.002   PHE B  75 
 TYR   0.016   0.002   TYR A 307 
 ARG   0.007   0.001   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 (  262)
  hydrogen bonds       : angle       6.95453 (  609)
  SS BOND              : bond        0.00332 (    7)
  SS BOND              : angle       0.84027 (   14)
  covalent geometry    : bond        0.00504 ( 9427)
  covalent geometry    : angle       0.62743 (12830)

*********************** 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
  42 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 21
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6007 (mm-30)
REVERT: A  229 MET cc_start: 0.9195 (mtm) cc_final: 0.8382 (mtm)
REVERT: B   37 MET cc_start: 0.7630 (tmm) cc_final: 0.6555 (tmm)
REVERT: D   61 MET cc_start: 0.9452 (pmm) cc_final: 0.8298 (pmm)
REVERT: D   84 MET cc_start: 0.9658 (mtm) cc_final: 0.9256 (mtm)
REVERT: E   48 MET cc_start: 0.8984 (mmm) cc_final: 0.8618 (mmt)
  outliers start: 21
  outliers final: 12
  residues processed: 41
  average time/residue: 0.2133
  time to fit residues: 13.5665
Evaluate side-chains
  32 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 19
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
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   74 ILE
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   52 SER
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  193 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0970
   chunk 85 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    2.3984

-------------------------------------------------------------------------------
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 323 GLN
B 207 GLN
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.032831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.025211 restraints weight = 173057.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.025831 restraints weight = 105301.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.026263 restraints weight = 73737.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9434  Z= 0.166
  Angle     :  0.560   9.202  12844  Z= 0.285
  Chirality :  0.042   0.135   1438
  Planarity :  0.004   0.035   1649
  Dihedral  :  5.103  77.919   1305
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.20 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.24), residues: 1210
  helix: -0.58 (0.53), residues: 100
  sheet: -1.90 (0.25), residues: 370
  loop : -1.45 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 160 
 HIS   0.005   0.001   HIS D 102 
 PHE   0.012   0.002   PHE B  75 
 TYR   0.013   0.001   TYR A 307 
 ARG   0.004   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02958 (  262)
  hydrogen bonds       : angle       6.47876 (  609)
  SS BOND              : bond        0.00207 (    7)
  SS BOND              : angle       0.69984 (   14)
  covalent geometry    : bond        0.00359 ( 9427)
  covalent geometry    : angle       0.55999 (12830)

*********************** 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
  43 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 20
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4918 (mm-30)
REVERT: A  174 MET cc_start: 0.8737 (ptm) cc_final: 0.8422 (ppp)
REVERT: B   37 MET cc_start: 0.7639 (tmm) cc_final: 0.6670 (tmm)
REVERT: D   61 MET cc_start: 0.9475 (pmm) cc_final: 0.8307 (pmm)
REVERT: D   84 MET cc_start: 0.9609 (mtm) cc_final: 0.9204 (mtm)
REVERT: E   48 MET cc_start: 0.8926 (mmm) cc_final: 0.8566 (mmm)
  outliers start: 23
  outliers final: 13
  residues processed: 40
  average time/residue: 0.1932
  time to fit residues: 12.2505
Evaluate side-chains
  33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 19
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
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   74 GLU
Chi-restraints excluded: chain A residue   81 MET
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 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   94 SER
Chi-restraints excluded: chain E residue   52 SER
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 65 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 86 optimal weight:    0.1980
   chunk 81 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 36 optimal weight:    0.2980
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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**
** 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 = 0.3343 r_free = 0.3343 target = 0.032972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.025335 restraints weight = 171912.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.025976 restraints weight = 103241.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.026394 restraints weight = 72051.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9434  Z= 0.123
  Angle     :  0.543   7.386  12844  Z= 0.275
  Chirality :  0.042   0.170   1438
  Planarity :  0.004   0.037   1649
  Dihedral  :  4.900  74.362   1305
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.18 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.24), residues: 1210
  helix: -0.37 (0.53), residues: 99
  sheet: -1.70 (0.25), residues: 381
  loop : -1.37 (0.24), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.011   0.001   PHE B  75 
 TYR   0.009   0.001   TYR A 307 
 ARG   0.003   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02648 (  262)
  hydrogen bonds       : angle       6.13137 (  609)
  SS BOND              : bond        0.00392 (    7)
  SS BOND              : angle       0.61313 (   14)
  covalent geometry    : bond        0.00273 ( 9427)
  covalent geometry    : angle       0.54285 (12830)

*********************** 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
  33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 19
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.4816 (mm-30)
REVERT: A  229 MET cc_start: 0.9007 (mtm) cc_final: 0.8049 (mtm)
REVERT: B   37 MET cc_start: 0.7611 (tmm) cc_final: 0.6863 (tmm)
REVERT: D   61 MET cc_start: 0.9473 (pmm) cc_final: 0.8264 (pmm)
REVERT: E   48 MET cc_start: 0.8948 (mmm) cc_final: 0.8601 (mmm)
  outliers start: 14
  outliers final: 12
  residues processed: 32
  average time/residue: 0.2076
  time to fit residues: 10.8125
Evaluate side-chains
  32 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 19
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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   74 GLU
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 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   52 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 81 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 3 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   overall best weight:    4.3788

-------------------------------------------------------------------------------
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**
** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.032862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.023936 restraints weight = 171924.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.024569 restraints weight = 107355.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.025005 restraints weight = 77620.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.5510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.091   9434  Z= 0.285
  Angle     :  0.682  10.159  12844  Z= 0.348
  Chirality :  0.043   0.132   1438
  Planarity :  0.005   0.041   1649
  Dihedral  :  5.597  73.590   1305
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 23.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.50 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.24), residues: 1210
  helix: -0.84 (0.51), residues: 99
  sheet: -1.87 (0.25), residues: 395
  loop : -1.31 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  47 
 HIS   0.007   0.002   HIS B  38 
 PHE   0.016   0.002   PHE B  75 
 TYR   0.015   0.002   TYR C 179 
 ARG   0.011   0.001   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  262)
  hydrogen bonds       : angle       6.81581 (  609)
  SS BOND              : bond        0.00385 (    7)
  SS BOND              : angle       0.93212 (   14)
  covalent geometry    : bond        0.00606 ( 9427)
  covalent geometry    : angle       0.68168 (12830)

*********************** 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: 29
    poor density    : 17
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.6827 (OUTLIER) cc_final: 0.6477 (t60)
REVERT: A  101 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6241 (tm-30)
REVERT: D   61 MET cc_start: 0.9535 (pmm) cc_final: 0.8108 (pmm)
REVERT: E   48 MET cc_start: 0.8894 (mmm) cc_final: 0.8471 (mmm)
  outliers start: 29
  outliers final: 20
  residues processed: 44
  average time/residue: 0.1864
  time to fit residues: 13.0289
Evaluate side-chains
  38 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 16
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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   47 TRP
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
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 C residue   21 THR
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   94 SER
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   52 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 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 = 0.3322 r_free = 0.3322 target = 0.032450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.025073 restraints weight = 176320.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.025682 restraints weight = 110452.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.026144 restraints weight = 70137.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.5427

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= 0.136
  Angle     :  0.575   8.332  12844  Z= 0.290
  Chirality :  0.043   0.147   1438
  Planarity :  0.004   0.037   1649
  Dihedral  :  5.194  65.964   1305
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 17.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.24), residues: 1210
  helix: -0.62 (0.53), residues: 99
  sheet: -1.62 (0.25), residues: 388
  loop : -1.24 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 321 
 PHE   0.013   0.001   PHE B  75 
 TYR   0.008   0.001   TYR B  40 
 ARG   0.004   0.001   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02748 (  262)
  hydrogen bonds       : angle       6.30943 (  609)
  SS BOND              : bond        0.00172 (    7)
  SS BOND              : angle       0.71818 (   14)
  covalent geometry    : bond        0.00303 ( 9427)
  covalent geometry    : angle       0.57438 (12830)

*********************** 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
  37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 19
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5763 (mm-30)
REVERT: A  101 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5799 (tm-30)
REVERT: A  174 MET cc_start: 0.8323 (ppp) cc_final: 0.7600 (ppp)
REVERT: B   37 MET cc_start: 0.7621 (tmm) cc_final: 0.6863 (tmm)
REVERT: D   61 MET cc_start: 0.9542 (pmm) cc_final: 0.8285 (pmm)
REVERT: E   48 MET cc_start: 0.8780 (mmm) cc_final: 0.8351 (mmm)
  outliers start: 18
  outliers final: 13
  residues processed: 35
  average time/residue: 0.1875
  time to fit residues: 10.8589
Evaluate side-chains
  33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 18
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
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 A residue  101 GLU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  275 ASN
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 E residue   52 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 116 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 62 optimal weight:   20.0000
   chunk 32 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 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 = 0.3315 r_free = 0.3315 target = 0.032270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.024969 restraints weight = 174401.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.025648 restraints weight = 110613.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.026090 restraints weight = 67796.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.5610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9434  Z= 0.158
  Angle     :  0.585  11.161  12844  Z= 0.294
  Chirality :  0.042   0.141   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  5.093  63.649   1305
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.24), residues: 1210
  helix: -0.60 (0.53), residues: 99
  sheet: -1.53 (0.26), residues: 388
  loop : -1.22 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.013   0.002   PHE B  75 
 TYR   0.008   0.001   TYR B  90 
 ARG   0.004   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02735 (  262)
  hydrogen bonds       : angle       6.16648 (  609)
  SS BOND              : bond        0.00171 (    7)
  SS BOND              : angle       0.65303 (   14)
  covalent geometry    : bond        0.00348 ( 9427)
  covalent geometry    : angle       0.58500 (12830)

*********************** 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
  38 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 18
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.6677 (OUTLIER) cc_final: 0.6421 (t60)
REVERT: A  101 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5803 (tm-30)
REVERT: A  206 MET cc_start: 0.8026 (tpp) cc_final: 0.7584 (tpp)
REVERT: D   61 MET cc_start: 0.9554 (pmm) cc_final: 0.8294 (pmm)
REVERT: E   48 MET cc_start: 0.8784 (mmm) cc_final: 0.8291 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 35
  average time/residue: 0.1871
  time to fit residues: 10.8813
Evaluate side-chains
  36 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 17
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
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   74 GLU
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 B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
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 E residue   52 SER
Chi-restraints excluded: chain E residue   70 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0970
   chunk 106 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 114 optimal weight:    0.0040
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0030
   chunk 104 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0370
   overall best weight:    0.2280

-------------------------------------------------------------------------------
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  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
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 = 0.3351 r_free = 0.3351 target = 0.032832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.025216 restraints weight = 172532.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.025856 restraints weight = 103045.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.026326 restraints weight = 71152.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.5401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9434  Z= 0.095
  Angle     :  0.554  10.293  12844  Z= 0.277
  Chirality :  0.043   0.152   1438
  Planarity :  0.004   0.039   1649
  Dihedral  :  4.730  54.105   1305
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.24), residues: 1210
  helix: -0.51 (0.54), residues: 99
  sheet: -1.52 (0.24), residues: 443
  loop : -1.12 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  53 
 HIS   0.002   0.001   HIS B 321 
 PHE   0.009   0.001   PHE B 262 
 TYR   0.008   0.001   TYR B  40 
 ARG   0.004   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02446 (  262)
  hydrogen bonds       : angle       5.64228 (  609)
  SS BOND              : bond        0.00255 (    7)
  SS BOND              : angle       0.78983 (   14)
  covalent geometry    : bond        0.00213 ( 9427)
  covalent geometry    : angle       0.55349 (12830)

********************** 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
  37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 20
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.6534 (OUTLIER) cc_final: 0.6303 (t60)
REVERT: A   74 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4561 (mm-30)
REVERT: A  101 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5262 (tm-30)
REVERT: B   37 MET cc_start: 0.7486 (tmm) cc_final: 0.7074 (tmm)
REVERT: D   61 MET cc_start: 0.9479 (pmm) cc_final: 0.8204 (pmm)
REVERT: E   48 MET cc_start: 0.9038 (mmm) cc_final: 0.8764 (mmm)
  outliers start: 17
  outliers final: 10
  residues processed: 36
  average time/residue: 0.1864
  time to fit residues: 10.9619
Evaluate side-chains
  31 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 18
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
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   74 GLU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  122 MET
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  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 4 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 98 optimal weight:   10.0000
   chunk 100 optimal weight:    0.7980
   chunk 119 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 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 = 0.3337 r_free = 0.3337 target = 0.032588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.024998 restraints weight = 171045.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.025604 restraints weight = 102236.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.026035 restraints weight = 71219.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9434  Z= 0.103
  Angle     :  0.529   7.176  12844  Z= 0.268
  Chirality :  0.042   0.150   1438
  Planarity :  0.004   0.042   1649
  Dihedral  :  4.595  48.818   1305
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 17.64 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.24), residues: 1210
  helix: -0.55 (0.53), residues: 97
  sheet: -1.36 (0.25), residues: 424
  loop : -1.04 (0.25), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  53 
 HIS   0.002   0.001   HIS B  38 
 PHE   0.010   0.001   PHE B  75 
 TYR   0.009   0.001   TYR B  40 
 ARG   0.002   0.000   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02400 (  262)
  hydrogen bonds       : angle       5.53029 (  609)
  SS BOND              : bond        0.00111 (    7)
  SS BOND              : angle       0.61475 (   14)
  covalent geometry    : bond        0.00234 ( 9427)
  covalent geometry    : angle       0.52899 (12830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3056.59 seconds
wall clock time: 54 minutes 24.03 seconds (3264.03 seconds total)