Starting phenix.real_space_refine
on Thu Feb 13 19:51:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8blq_16113/02_2025/8blq_16113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8blq_16113/02_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_16113/02_2025/8blq_16113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8blq_16113/02_2025/8blq_16113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8blq_16113/02_2025/8blq_16113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8blq_16113/02_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-5592/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: 6.11, per 1000 atoms: 0.66
  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: 1.39
  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: 3.17

  Time building geometry restraints manager: 2.48 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:             3.160
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     24.730
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.310
-------------------------------------------------------------------------------
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   9427  Z= 0.146
  Angle     :  0.551   7.007  12830  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 

*********************** 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  : 1.058 
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: 0.3201
  time to fit residues: 25.6831
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  : 1.039 
-------------------------------------------------------------------------------
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 = 0.033599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.023901 restraints weight = 152942.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.024415 restraints weight = 101656.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.024915 restraints weight = 77763.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.118   9427  Z= 0.458
  Angle     :  0.775  11.032  12830  Z= 0.400
  Chirality :  0.044   0.152   1438
  Planarity :  0.005   0.061   1649
  Dihedral  :  5.465  89.758   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 

*********************** 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  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8856 (mp10)
REVERT: A   74 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6077 (mm-30)
REVERT: A  285 TRP cc_start: 0.9084 (m100) cc_final: 0.8613 (m100)
REVERT: D   61 MET cc_start: 0.9443 (pmm) cc_final: 0.9021 (pmm)
REVERT: D   84 MET cc_start: 0.9688 (mtm) cc_final: 0.9002 (mtm)
  outliers start: 16
  outliers final: 7
  residues processed: 42
  average time/residue: 0.2381
  time to fit residues: 15.0211
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  : 1.045 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 25 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A   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
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.033674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.025731 restraints weight = 171567.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.026372 restraints weight = 104922.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.026853 restraints weight = 73479.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9427  Z= 0.173
  Angle     :  0.542   8.118  12830  Z= 0.278
  Chirality :  0.043   0.137   1438
  Planarity :  0.004   0.036   1649
  Dihedral  :  4.953  86.751   1305
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.16 %
    Favored  : 86.06 %
  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: -2.71 (0.23), residues: 1210
  helix: -0.73 (0.54), residues: 99
  sheet: -2.17 (0.25), residues: 377
  loop : -1.75 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 160 
 HIS   0.002   0.001   HIS B  38 
 PHE   0.023   0.002   PHE B 239 
 TYR   0.010   0.001   TYR A 307 
 ARG   0.004   0.000   ARG A  84 

*********************** 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
  31 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8796 (mp10)
REVERT: A  229 MET cc_start: 0.9289 (mtm) cc_final: 0.9086 (mtm)
REVERT: B   37 MET cc_start: 0.7624 (tmm) cc_final: 0.6336 (tmm)
REVERT: D   61 MET cc_start: 0.9347 (pmm) cc_final: 0.8269 (pmm)
REVERT: D   84 MET cc_start: 0.9600 (mtm) cc_final: 0.9206 (mtm)
REVERT: D  102 HIS cc_start: 0.9351 (p-80) cc_final: 0.9113 (p-80)
  outliers start: 8
  outliers final: 6
  residues processed: 30
  average time/residue: 0.2317
  time to fit residues: 10.8938
Evaluate side-chains
  26 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain D residue   94 SER
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:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0170
   chunk 79 optimal weight:    8.9990
   chunk 102 optimal weight:    7.9990
   overall best weight:    3.2026

-------------------------------------------------------------------------------
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  65 GLN
A 295 HIS
B 207 GLN
B 260 ASN
B 261 ASN
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.033481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.024154 restraints weight = 167707.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.024836 restraints weight = 104112.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.025309 restraints weight = 74501.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9427  Z= 0.300
  Angle     :  0.597   9.929  12830  Z= 0.306
  Chirality :  0.042   0.150   1438
  Planarity :  0.004   0.040   1649
  Dihedral  :  5.182  84.125   1305
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.55 %
    Favored  : 84.80 %
  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: -0.72 (0.53), residues: 99
  sheet: -2.08 (0.25), residues: 383
  loop : -1.50 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 271 
 HIS   0.004   0.001   HIS A 331 
 PHE   0.016   0.002   PHE B 239 
 TYR   0.015   0.002   TYR A 307 
 ARG   0.006   0.001   ARG B 334 

*********************** 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
  38 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 21
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5446 (mm-30)
REVERT: A  174 MET cc_start: 0.8878 (ptm) cc_final: 0.8344 (ppp)
REVERT: B   37 MET cc_start: 0.7608 (tmm) cc_final: 0.6364 (tmm)
REVERT: D   61 MET cc_start: 0.9432 (pmm) cc_final: 0.8296 (pmm)
REVERT: D   84 MET cc_start: 0.9653 (mtm) cc_final: 0.9039 (mtm)
REVERT: E   48 MET cc_start: 0.9128 (mmm) cc_final: 0.8158 (mmm)
  outliers start: 17
  outliers final: 9
  residues processed: 37
  average time/residue: 0.2151
  time to fit residues: 12.5159
Evaluate side-chains
  30 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0020
   chunk 7 optimal weight:    6.9990
   chunk 85 optimal weight:    0.2980
   chunk 17 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.4594

-------------------------------------------------------------------------------
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 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.033720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.024352 restraints weight = 167065.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.025046 restraints weight = 103330.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.025547 restraints weight = 73460.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9427  Z= 0.171
  Angle     :  0.530   8.025  12830  Z= 0.270
  Chirality :  0.042   0.134   1438
  Planarity :  0.004   0.037   1649
  Dihedral  :  4.907  79.443   1305
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.72 %
    Favored  : 83.24 %
  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: -2.22 (0.24), residues: 1210
  helix: -0.45 (0.54), residues: 99
  sheet: -1.85 (0.25), residues: 376
  loop : -1.39 (0.23), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 160 
 HIS   0.002   0.001   HIS B  38 
 PHE   0.012   0.001   PHE B 239 
 TYR   0.010   0.001   TYR A 307 
 ARG   0.003   0.000   ARG E 106 

*********************** 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
  42 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 21
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 MET cc_start: 0.7530 (tmm) cc_final: 0.6625 (tmm)
REVERT: D   61 MET cc_start: 0.9462 (pmm) cc_final: 0.8223 (pmm)
REVERT: D   84 MET cc_start: 0.9601 (mtm) cc_final: 0.9238 (mtm)
REVERT: E   48 MET cc_start: 0.9152 (mmm) cc_final: 0.8780 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 40
  average time/residue: 0.2171
  time to fit residues: 13.2173
Evaluate side-chains
  31 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 19
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   11 LEU
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   30 THR
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:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 90 optimal weight:    9.9990
   chunk 86 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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**
** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.033588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.024302 restraints weight = 167287.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.024992 restraints weight = 102273.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.025500 restraints weight = 72502.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9427  Z= 0.173
  Angle     :  0.527   7.064  12830  Z= 0.268
  Chirality :  0.042   0.182   1438
  Planarity :  0.004   0.039   1649
  Dihedral  :  4.747  76.349   1305
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.40 %
    Favored  : 82.94 %
  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: -2.02 (0.24), residues: 1210
  helix: -0.38 (0.54), residues: 99
  sheet: -1.65 (0.25), residues: 391
  loop : -1.26 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  50 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.010   0.001   PHE B  75 
 TYR   0.013   0.001   TYR A 307 
 ARG   0.003   0.000   ARG B 334 

*********************** 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
  36 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8744 (ptm) cc_final: 0.8342 (ppp)
REVERT: A  229 MET cc_start: 0.9190 (mtm) cc_final: 0.8916 (mtm)
REVERT: B   37 MET cc_start: 0.7526 (tmm) cc_final: 0.6674 (tmm)
REVERT: D   61 MET cc_start: 0.9478 (pmm) cc_final: 0.8184 (pmm)
REVERT: E   48 MET cc_start: 0.9181 (mmm) cc_final: 0.8785 (mmm)
  outliers start: 17
  outliers final: 14
  residues processed: 35
  average time/residue: 0.2093
  time to fit residues: 11.6322
Evaluate side-chains
  32 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 18
  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  328 ASN
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 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  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:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.032960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.024162 restraints weight = 171501.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.024712 restraints weight = 121221.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.025246 restraints weight = 79022.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9427  Z= 0.369
  Angle     :  0.679  10.282  12830  Z= 0.345
  Chirality :  0.044   0.272   1438
  Planarity :  0.005   0.044   1649
  Dihedral  :  5.539  74.389   1305
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 23.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.79 %
    Favored  : 82.16 %
  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: -2.19 (0.24), residues: 1210
  helix: -0.87 (0.52), residues: 99
  sheet: -1.80 (0.24), residues: 407
  loop : -1.26 (0.24), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 271 
 HIS   0.006   0.002   HIS B  38 
 PHE   0.016   0.002   PHE B  75 
 TYR   0.016   0.002   TYR C 179 
 ARG   0.008   0.001   ARG D  83 

*********************** 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
  40 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 19
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6177 (tm-30)
REVERT: A  206 MET cc_start: 0.7671 (tpp) cc_final: 0.7441 (tpp)
REVERT: D   61 MET cc_start: 0.9524 (pmm) cc_final: 0.8121 (pmm)
  outliers start: 21
  outliers final: 16
  residues processed: 38
  average time/residue: 0.1916
  time to fit residues: 11.9506
Evaluate side-chains
  36 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
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 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  169 THR
Chi-restraints excluded: chain E residue  191 VAL
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  220 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 98 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.4384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.032657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.025103 restraints weight = 174966.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.025737 restraints weight = 103524.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.026202 restraints weight = 71831.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.5205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9427  Z= 0.170
  Angle     :  0.554   7.544  12830  Z= 0.280
  Chirality :  0.043   0.156   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  4.962  64.566   1305
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.18 %
    Favored  : 81.97 %
  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: -1.98 (0.24), residues: 1210
  helix: -0.55 (0.53), residues: 99
  sheet: -1.60 (0.25), residues: 386
  loop : -1.22 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 321 
 PHE   0.011   0.001   PHE B  75 
 TYR   0.008   0.001   TYR A 105 
 ARG   0.003   0.000   ARG B 334 

*********************** 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
  38 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 19
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5537 (tm-30)
REVERT: A  229 MET cc_start: 0.8913 (mtm) cc_final: 0.8695 (mtm)
REVERT: B   37 MET cc_start: 0.7679 (tmm) cc_final: 0.6901 (tmm)
REVERT: D   61 MET cc_start: 0.9505 (pmm) cc_final: 0.8245 (pmm)
REVERT: E   48 MET cc_start: 0.8945 (mmm) cc_final: 0.8713 (mmm)
  outliers start: 19
  outliers final: 13
  residues processed: 36
  average time/residue: 0.2003
  time to fit residues: 11.4703
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  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  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:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 116 optimal weight:    0.4980
   chunk 100 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.032851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.023956 restraints weight = 169095.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.024598 restraints weight = 105446.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.025041 restraints weight = 76054.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9427  Z= 0.278
  Angle     :  0.608   9.542  12830  Z= 0.307
  Chirality :  0.042   0.157   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  5.205  64.545   1305
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 19.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.57 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.99 (0.24), residues: 1210
  helix: -0.59 (0.54), residues: 99
  sheet: -1.68 (0.25), residues: 403
  loop : -1.14 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  47 
 HIS   0.005   0.001   HIS B  38 
 PHE   0.013   0.002   PHE B  75 
 TYR   0.009   0.001   TYR B  90 
 ARG   0.005   0.001   ARG B 334 

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

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 19
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6015 (tm-30)
REVERT: A  229 MET cc_start: 0.8906 (mtm) cc_final: 0.8629 (mtm)
REVERT: B   37 MET cc_start: 0.7649 (tmm) cc_final: 0.6842 (tmm)
REVERT: D   61 MET cc_start: 0.9537 (pmm) cc_final: 0.8103 (pmm)
REVERT: E   48 MET cc_start: 0.8885 (mmm) cc_final: 0.8628 (mmm)
  outliers start: 16
  outliers final: 14
  residues processed: 32
  average time/residue: 0.1969
  time to fit residues: 10.3725
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  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   30 THR
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:   10.0000
   chunk 72 optimal weight:    0.2980
   chunk 106 optimal weight:   10.0000
   chunk 88 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 114 optimal weight:    0.0070
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:   30.0000
   chunk 104 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.2602

-------------------------------------------------------------------------------
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
B 281 ASN
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.032547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.024967 restraints weight = 174437.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.025612 restraints weight = 103655.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.026070 restraints weight = 71696.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9427  Z= 0.167
  Angle     :  0.555   6.983  12830  Z= 0.281
  Chirality :  0.043   0.150   1438
  Planarity :  0.004   0.038   1649
  Dihedral  :  4.905  57.829   1305
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 17.06 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.89 (0.24), residues: 1210
  helix: -0.46 (0.54), residues: 99
  sheet: -1.54 (0.25), residues: 412
  loop : -1.13 (0.24), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  47 
 HIS   0.004   0.001   HIS B 321 
 PHE   0.011   0.001   PHE B  75 
 TYR   0.007   0.001   TYR B  36 
 ARG   0.003   0.000   ARG A 190 

********************** 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
  33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 19
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5492 (tm-30)
REVERT: B   37 MET cc_start: 0.7596 (tmm) cc_final: 0.6942 (tmm)
REVERT: D   61 MET cc_start: 0.9494 (pmm) cc_final: 0.8200 (pmm)
REVERT: E   48 MET cc_start: 0.8988 (mmm) cc_final: 0.8767 (mmm)
  outliers start: 14
  outliers final: 13
  residues processed: 31
  average time/residue: 0.1943
  time to fit residues: 9.9638
Evaluate side-chains
  32 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 18
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain B residue    5 THR
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 60 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3331 r_free = 0.3331 target = 0.032532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.024999 restraints weight = 171729.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.025625 restraints weight = 102096.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.026037 restraints weight = 71035.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9427  Z= 0.167
  Angle     :  0.546   7.299  12830  Z= 0.277
  Chirality :  0.042   0.148   1438
  Planarity :  0.004   0.040   1649
  Dihedral  :  4.727  53.114   1305
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 17.25 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.89 (0.24), residues: 1210
  helix: -0.51 (0.54), residues: 99
  sheet: -1.50 (0.24), residues: 437
  loop : -1.12 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  47 
 HIS   0.003   0.001   HIS B 321 
 PHE   0.010   0.001   PHE B  75 
 TYR   0.007   0.001   TYR B 205 
 ARG   0.004   0.000   ARG D  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.44 seconds
wall clock time: 55 minutes 32.84 seconds (3332.84 seconds total)