Starting phenix.real_space_refine
on Wed Mar  4 00:09:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2026/6uva_20906.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    6095      2.51       5
     N    1657      2.21       5
     O    1737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9561
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1604
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 6, 'TRANS': 183}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 380
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "E"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
    Chain: "P"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 326
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 4, 'TRANS': 38}
    Chain: "R"
      Number of atoms: 2819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2819
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 9, 'TRANS': 334}
          Chain breaks: 4
  Time building chain proxies: 2.30, per 1000 atoms: 0.24
  Number of scatterers: 9561
  At special positions: 0
  Unit cell: (115.37, 97.11, 146.08, 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      72     16.00
     O    1737      8.00
     N    1657      7.00
     C    6095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  40 " - pdb=" SG  CYS E  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  57 " - pdb=" SG  CYS E 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  10 " - pdb=" SG  CYS P  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  65 " - pdb=" SG  CYS R 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  88 " - pdb=" SG  CYS R 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 212 " - pdb=" SG  CYS R 282 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 326.5 milliseconds
  

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2258

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      40.2% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.803A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.637A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.746A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.788A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 15 through 23
    Processing helix  chain 'G' and resid 29 through 43
      removed outlier: 3.509A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.714A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'E' and resid 36 through 48
      removed outlier: 4.188A  pdb=" N   CYS E  40 " --> pdb=" O   ARG E  36 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA E  43 " --> pdb=" O   LEU E  39 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 58
      removed outlier: 3.632A  pdb=" N   TRP E  56 " --> pdb=" O   VAL E  53 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   CYS E  57 " --> pdb=" O   TRP E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 76
    Processing helix  chain 'E' and resid 86 through 99
      removed outlier: 4.531A  pdb=" N   GLY E  91 " --> pdb=" O   PRO E  87 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   PHE E  92 " --> pdb=" O   LEU E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 142
      Proline residue:  E 126  - end of helix
      removed outlier: 3.951A  pdb=" N   LYS E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 15 through 28
    Processing helix  chain 'R' and resid 36 through 52
    Processing helix  chain 'R' and resid 124 through 128
      removed outlier: 3.551A  pdb=" N   CYS R 127 " --> pdb=" O   TYR R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 167
      removed outlier: 3.707A  pdb=" N   LYS R 134 " --> pdb=" O   ASN R 130 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS R 167 " --> pdb=" O   PHE R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 198
    Processing helix  chain 'R' and resid 204 through 208
      removed outlier: 4.205A  pdb=" N   THR R 207 " --> pdb=" O   LEU R 204 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN R 208 " --> pdb=" O   VAL R 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 204 through 208'
    Processing helix  chain 'R' and resid 210 through 242
    Processing helix  chain 'R' and resid 252 through 261
    Processing helix  chain 'R' and resid 263 through 277
    Processing helix  chain 'R' and resid 280 through 284
      removed outlier: 3.670A  pdb=" N   TRP R 283 " --> pdb=" O   ASP R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 290
      No H-bonds generated for 'chain 'R' and resid 288 through 290'
    Processing helix  chain 'R' and resid 291 through 321
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 330 through 346
      Proline residue:  R 343  - end of helix
    Processing helix  chain 'R' and resid 347 through 350
    Processing helix  chain 'R' and resid 363 through 385
      removed outlier: 5.205A  pdb=" N   GLY R 377 " --> pdb=" O   MET R 373 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   LEU R 378 " --> pdb=" O   HIS R 374 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 388 through 399
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.970A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.350A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.528A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.501A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.670A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.202A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.775A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.523A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.527A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.672A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 84 through 87

    456 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3099
        1.34 -     1.46: 2237
        1.46 -     1.58: 4344
        1.58 -     1.70: 0
        1.70 -     1.81: 100
  Bond restraints: 9780
  Sorted by residual:
  bond pdb=" C   ASP P  40 "
       pdb=" N   PRO P  41 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.023 2.34e-02 1.83e+03 9.30e-01
  bond pdb=" CA  GLY B 244 "
       pdb=" C   GLY B 244 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 7.45e-01
  bond pdb=" CA  GLU E  74 "
       pdb=" C   GLU E  74 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.28e-02 6.10e+03 6.82e-01
  bond pdb=" C   VAL E 124 "
       pdb=" N   ILE E 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.338 -0.009 1.13e-02 7.83e+03 6.31e-01
  bond pdb=" CA  VAL E  51 "
       pdb=" CB  VAL E  51 "
    ideal  model  delta    sigma   weight residual
    1.538  1.546 -0.008 1.10e-02 8.26e+03 5.83e-01
  ... (remaining 9775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 13037
        1.66 -     3.32: 181
        3.32 -     4.98: 33
        4.98 -     6.64: 9
        6.64 -     8.31: 2
  Bond angle restraints: 13262
  Sorted by residual:
  angle pdb=" CA  TYR R 367 "
        pdb=" CB  TYR R 367 "
        pdb=" CG  TYR R 367 "
      ideal   model   delta    sigma   weight residual
     113.90  119.60   -5.70 1.80e+00 3.09e-01 1.00e+01
  angle pdb=" N   VAL R 205 "
        pdb=" CA  VAL R 205 "
        pdb=" C   VAL R 205 "
      ideal   model   delta    sigma   weight residual
     112.29  109.46    2.83 9.40e-01 1.13e+00 9.08e+00
  angle pdb=" C   THR E  73 "
        pdb=" N   GLU E  74 "
        pdb=" CA  GLU E  74 "
      ideal   model   delta    sigma   weight residual
     122.37  118.02    4.35 1.54e+00 4.22e-01 7.97e+00
  angle pdb=" C   PHE R 166 "
        pdb=" N   LYS R 167 "
        pdb=" CA  LYS R 167 "
      ideal   model   delta    sigma   weight residual
     121.54  126.14   -4.60 1.91e+00 2.74e-01 5.81e+00
  angle pdb=" CA  LEU R 395 "
        pdb=" CB  LEU R 395 "
        pdb=" CG  LEU R 395 "
      ideal   model   delta    sigma   weight residual
     116.30  124.61   -8.31 3.50e+00 8.16e-02 5.63e+00
  ... (remaining 13257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4970
       17.98 -    35.96: 561
       35.96 -    53.94: 193
       53.94 -    71.92: 49
       71.92 -    89.89: 15
  Dihedral angle restraints: 5788
    sinusoidal: 2300
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" CB  CYS E  57 "
           pdb=" SG  CYS E  57 "
           pdb=" SG  CYS E 104 "
           pdb=" CB  CYS E 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.11   81.11     1      1.00e+01 1.00e-02 8.12e+01
  dihedral pdb=" CB  CYS R  88 "
           pdb=" SG  CYS R  88 "
           pdb=" SG  CYS R 127 "
           pdb=" CB  CYS R 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.59  -49.59     1      1.00e+01 1.00e-02 3.38e+01
  dihedral pdb=" CB  CYS R  48 "
           pdb=" SG  CYS R  48 "
           pdb=" SG  CYS R  74 "
           pdb=" CB  CYS R  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.92   40.08     1      1.00e+01 1.00e-02 2.25e+01
  ... (remaining 5785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 915
       0.030 -    0.060: 377
       0.060 -    0.091: 109
       0.091 -    0.121: 68
       0.121 -    0.151: 6
  Chirality restraints: 1475
  Sorted by residual:
  chirality pdb=" CA  LYS E  42 "
            pdb=" N   LYS E  42 "
            pdb=" C   LYS E  42 "
            pdb=" CB  LYS E  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE R 352 "
            pdb=" N   ILE R 352 "
            pdb=" C   ILE R 352 "
            pdb=" CB  ILE R 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  ILE E 123 "
            pdb=" N   ILE E 123 "
            pdb=" C   ILE E 123 "
            pdb=" CB  ILE E 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1472 not shown)

  Planarity restraints: 1684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 367 "    0.016 2.00e-02 2.50e+03   1.22e-02 2.99e+00
        pdb=" CG  TYR R 367 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 367 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 367 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 367 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 367 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 367 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 367 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 114 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO E 115 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO E 115 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 115 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 113 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO E 114 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO E 114 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 114 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1681 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 887
        2.75 -     3.28: 9414
        3.28 -     3.82: 16408
        3.82 -     4.36: 19653
        4.36 -     4.90: 32748
  Nonbonded interactions: 79110
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   TRP R  72 "
            pdb=" OH  TYR R  91 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" O   PRO N 100 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   HIS R 370 "
            pdb=" ND1 HIS R 374 "
     model   vdw
     2.321 3.120
  ... (remaining 79105 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.330
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:10.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
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   0.030   9789  Z= 0.116
  Angle     :  0.549   8.305  13280  Z= 0.314
  Chirality :  0.040   0.151   1475
  Planarity :  0.003   0.033   1684
  Dihedral  : 18.040  89.894   3503
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 26.30 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.22), residues: 1169
  helix: -0.89 (0.22), residues: 434
  sheet: -1.42 (0.30), residues: 225
  loop : -2.05 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 129 
 TYR   0.030   0.001   TYR R 367 
 PHE   0.011   0.001   PHE R 308 
 TRP   0.007   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9780)
  covalent geometry    : angle       0.54734 (13262)
  SS BOND              : bond        0.00292 (    9)
  SS BOND              : angle       1.25141 (   18)
  hydrogen bonds       : bond        0.17586 (  456)
  hydrogen bonds       : angle       6.82122 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.5897 (pmtt) cc_final: 0.5426 (mmtm)
REVERT: B   96 ARG cc_start: 0.6594 (mtm180) cc_final: 0.6373 (mtm110)
REVERT: B  134 ARG cc_start: 0.6435 (ptp-110) cc_final: 0.6043 (ppt170)
REVERT: E  142 LYS cc_start: 0.5737 (mtmp) cc_final: 0.5498 (mtmt)
REVERT: R   42 MET cc_start: 0.3583 (mtm) cc_final: 0.3214 (ttm)
REVERT: R  339 LEU cc_start: 0.7314 (mp) cc_final: 0.7093 (mm)
  outliers start: 35
  outliers final: 9
  residues processed: 164
  average time/residue: 0.7049
  time to fit residues: 122.2628
Evaluate side-chains
  115 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   72 CYS
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   98 SER
Chi-restraints excluded: chain R residue  136 LYS
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  342 VAL
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  351 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 218 ASN
A 267 GLN
A 357 HIS
A 387 HIS
B  88 ASN
B 259 GLN
N  82 GLN
E  86 ASN
E 110 HIS
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 250 GLN
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.221928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.178436 restraints weight = 10052.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 1.38
r_work: 0.3849 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9789  Z= 0.157
  Angle     :  0.608   7.971  13280  Z= 0.323
  Chirality :  0.044   0.148   1475
  Planarity :  0.004   0.038   1684
  Dihedral  :  5.679  49.992   1312
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.76 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.23), residues: 1169
  helix:  0.29 (0.24), residues: 441
  sheet: -0.83 (0.30), residues: 236
  loop : -1.56 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 137 
 TYR   0.010   0.001   TYR R 227 
 PHE   0.015   0.002   PHE E 100 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.006   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9780)
  covalent geometry    : angle       0.60524 (13262)
  SS BOND              : bond        0.00173 (    9)
  SS BOND              : angle       1.55159 (   18)
  hydrogen bonds       : bond        0.05011 (  456)
  hydrogen bonds       : angle       5.10752 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 113
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6417 (mm-40)
REVERT: A  216 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.5956 (mmtm)
REVERT: A  317 ARG cc_start: 0.5244 (mtm180) cc_final: 0.4821 (mmt-90)
REVERT: A  344 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7018 (mm-30)
REVERT: B   46 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7449 (mpt-90)
REVERT: B   96 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7348 (ttm170)
REVERT: B  132 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5680 (m-40)
REVERT: B  134 ARG cc_start: 0.6925 (ptp-110) cc_final: 0.5883 (ppt170)
REVERT: B  219 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7628 (mtt180)
REVERT: N   83 MET cc_start: 0.6897 (mtp) cc_final: 0.6621 (mtm)
REVERT: E  118 VAL cc_start: 0.5707 (t) cc_final: 0.5399 (t)
REVERT: P   18 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7165 (mp10)
REVERT: R   42 MET cc_start: 0.4612 (mtm) cc_final: 0.4107 (ttm)
REVERT: R   53 MET cc_start: 0.3183 (ptm) cc_final: 0.2453 (ptm)
REVERT: R  303 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: R  339 LEU cc_start: 0.7363 (mp) cc_final: 0.7120 (mm)
  outliers start: 47
  outliers final: 15
  residues processed: 149
  average time/residue: 0.6476
  time to fit residues: 102.1606
Evaluate side-chains
  125 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain E residue   72 CYS
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  303 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 259 GLN
B 266 HIS
N  35 ASN
E  71 ASN
E  86 ASN
E  97 HIS
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.217752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.166364 restraints weight = 9701.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.41
r_work: 0.3780 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9789  Z= 0.139
  Angle     :  0.578   7.110  13280  Z= 0.307
  Chirality :  0.043   0.146   1475
  Planarity :  0.004   0.040   1684
  Dihedral  :  4.931  34.199   1300
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 24.66 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.24), residues: 1169
  helix:  0.85 (0.25), residues: 443
  sheet: -0.50 (0.31), residues: 247
  loop : -1.28 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 137 
 TYR   0.010   0.001   TYR R 227 
 PHE   0.012   0.001   PHE E 100 
 TRP   0.017   0.002   TRP E 139 
 HIS   0.010   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9780)
  covalent geometry    : angle       0.57633 (13262)
  SS BOND              : bond        0.00217 (    9)
  SS BOND              : angle       1.47099 (   18)
  hydrogen bonds       : bond        0.04710 (  456)
  hydrogen bonds       : angle       4.82163 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 112
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6875 (mm-40) cc_final: 0.6372 (mm-40)
REVERT: A  216 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6088 (mmtm)
REVERT: A  264 ASN cc_start: 0.4964 (OUTLIER) cc_final: 0.4755 (t0)
REVERT: A  344 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (mm-30)
REVERT: B   59 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7967 (m-80)
REVERT: B   96 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7094 (mmt-90)
REVERT: B  134 ARG cc_start: 0.6830 (ptp-110) cc_final: 0.5694 (ppt170)
REVERT: B  146 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8209 (mm)
REVERT: B  266 HIS cc_start: 0.7271 (t-90) cc_final: 0.6885 (t70)
REVERT: G   46 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6719 (mmtp)
REVERT: N   67 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6958 (mtp85)
REVERT: N   83 MET cc_start: 0.6910 (mtp) cc_final: 0.6606 (mtm)
REVERT: E   75 MET cc_start: 0.2621 (OUTLIER) cc_final: 0.2374 (mpm)
REVERT: E   97 HIS cc_start: 0.3416 (OUTLIER) cc_final: 0.2882 (t-170)
REVERT: E  118 VAL cc_start: 0.5593 (t) cc_final: 0.5283 (t)
REVERT: E  139 TRP cc_start: 0.5979 (t60) cc_final: 0.5684 (t60)
REVERT: E  140 ARG cc_start: 0.5456 (OUTLIER) cc_final: 0.4267 (mmm160)
REVERT: P   18 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7135 (mp10)
REVERT: R   42 MET cc_start: 0.4430 (mtm) cc_final: 0.3991 (ttm)
REVERT: R   53 MET cc_start: 0.2920 (ptm) cc_final: 0.2404 (ptm)
REVERT: R  303 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7734 (mp)
REVERT: R  339 LEU cc_start: 0.7407 (mp) cc_final: 0.7169 (mm)
  outliers start: 55
  outliers final: 14
  residues processed: 153
  average time/residue: 0.6699
  time to fit residues: 108.4478
Evaluate side-chains
  133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  303 LEU
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  351 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    0.3980
   chunk 96 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 155 ASN
B 176 GLN
B 220 GLN
B 340 ASN
G  59 ASN
N  35 ASN
E  71 ASN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 187 ASN
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.217876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.166740 restraints weight = 9768.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.29
r_work: 0.3789 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9789  Z= 0.132
  Angle     :  0.566   7.215  13280  Z= 0.300
  Chirality :  0.043   0.142   1475
  Planarity :  0.004   0.041   1684
  Dihedral  :  4.837  26.382   1299
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 24.66 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.24), residues: 1169
  helix:  1.06 (0.25), residues: 443
  sheet: -0.29 (0.31), residues: 245
  loop : -1.23 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  72 
 TYR   0.010   0.001   TYR R 227 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9780)
  covalent geometry    : angle       0.56391 (13262)
  SS BOND              : bond        0.00268 (    9)
  SS BOND              : angle       1.48810 (   18)
  hydrogen bonds       : bond        0.04541 (  456)
  hydrogen bonds       : angle       4.71320 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 112
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6458 (mm-40)
REVERT: A  216 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6017 (mmtm)
REVERT: A  264 ASN cc_start: 0.4950 (OUTLIER) cc_final: 0.4667 (t0)
REVERT: A  344 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7155 (mm-30)
REVERT: B   59 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7917 (m-80)
REVERT: B  134 ARG cc_start: 0.6771 (ptp-110) cc_final: 0.5675 (ppt170)
REVERT: B  146 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8189 (mm)
REVERT: B  266 HIS cc_start: 0.7446 (t-90) cc_final: 0.7040 (t70)
REVERT: G   46 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6708 (mmtp)
REVERT: N   83 MET cc_start: 0.6871 (mtp) cc_final: 0.6590 (mtm)
REVERT: E   71 ASN cc_start: 0.2228 (OUTLIER) cc_final: 0.1760 (m-40)
REVERT: E   75 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.2154 (mpm)
REVERT: E   97 HIS cc_start: 0.3535 (OUTLIER) cc_final: 0.3326 (t70)
REVERT: E  118 VAL cc_start: 0.5571 (OUTLIER) cc_final: 0.5233 (t)
REVERT: E  140 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4159 (mmm160)
REVERT: P   18 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7161 (mp10)
REVERT: R   42 MET cc_start: 0.4443 (mtm) cc_final: 0.3999 (ttm)
REVERT: R   53 MET cc_start: 0.3043 (ptm) cc_final: 0.2666 (ptm)
REVERT: R  303 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7896 (mt)
REVERT: R  339 LEU cc_start: 0.7385 (mp) cc_final: 0.7154 (mm)
  outliers start: 54
  outliers final: 27
  residues processed: 152
  average time/residue: 0.6585
  time to fit residues: 106.2131
Evaluate side-chains
  147 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain E residue   71 ASN
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain E residue  102 SER
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain E residue  143 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  136 LYS
Chi-restraints excluded: chain R residue  169 LEU
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  303 LEU
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  314 ARG
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 113 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B  32 GLN
B 176 GLN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 172 GLN
** R 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.217612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.167748 restraints weight = 9750.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.49
r_work: 0.3723 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9789  Z= 0.131
  Angle     :  0.562   6.877  13280  Z= 0.298
  Chirality :  0.043   0.143   1475
  Planarity :  0.004   0.042   1684
  Dihedral  :  4.835  25.711   1299
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 24.57 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.25), residues: 1169
  helix:  1.17 (0.25), residues: 443
  sheet: -0.32 (0.31), residues: 254
  loop : -1.10 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  72 
 TYR   0.010   0.001   TYR A 391 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.017   0.001   TRP E 139 
 HIS   0.008   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9780)
  covalent geometry    : angle       0.56026 (13262)
  SS BOND              : bond        0.00212 (    9)
  SS BOND              : angle       1.43214 (   18)
  hydrogen bonds       : bond        0.04465 (  456)
  hydrogen bonds       : angle       4.67089 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 110
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6345 (mm-40)
REVERT: A  216 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6173 (mmtm)
REVERT: A  264 ASN cc_start: 0.5046 (OUTLIER) cc_final: 0.4807 (t0)
REVERT: A  344 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7184 (mm-30)
REVERT: A  389 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7670 (ttm110)
REVERT: A  392 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7764 (mt-10)
REVERT: B   59 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7926 (m-80)
REVERT: B  134 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.5605 (ppt170)
REVERT: B  146 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8230 (mm)
REVERT: B  266 HIS cc_start: 0.7424 (t-90) cc_final: 0.6966 (t70)
REVERT: G   46 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6766 (mmtp)
REVERT: N   83 MET cc_start: 0.6869 (mtp) cc_final: 0.6557 (mtm)
REVERT: E   62 PHE cc_start: 0.1884 (OUTLIER) cc_final: 0.1303 (p90)
REVERT: E   75 MET cc_start: 0.2525 (OUTLIER) cc_final: 0.1574 (tmm)
REVERT: E  118 VAL cc_start: 0.5576 (OUTLIER) cc_final: 0.5235 (t)
REVERT: E  140 ARG cc_start: 0.5445 (OUTLIER) cc_final: 0.4239 (mmm160)
REVERT: P   18 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7248 (mp10)
REVERT: R  177 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.7601 (m-70)
  outliers start: 58
  outliers final: 29
  residues processed: 154
  average time/residue: 0.6434
  time to fit residues: 105.3810
Evaluate side-chains
  148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 107
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  102 SER
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain E residue  143 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue   85 MET
Chi-restraints excluded: chain R residue  136 LYS
Chi-restraints excluded: chain R residue  177 HIS
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  314 ARG
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 357 HIS
B 176 GLN
B 340 ASN
E  71 ASN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 130 ASN
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 200 ASN
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.212446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.162700 restraints weight = 9696.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 1.46
r_work: 0.3664 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9789  Z= 0.275
  Angle     :  0.764  10.285  13280  Z= 0.410
  Chirality :  0.050   0.231   1475
  Planarity :  0.006   0.050   1684
  Dihedral  :  5.841  35.243   1299
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 23.80 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.24), residues: 1169
  helix:  0.76 (0.24), residues: 434
  sheet: -0.26 (0.32), residues: 235
  loop : -1.22 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N  72 
 TYR   0.013   0.002   TYR G  40 
 PHE   0.017   0.003   PHE B 199 
 TRP   0.022   0.003   TRP E 139 
 HIS   0.007   0.002   HIS R 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 9780)
  covalent geometry    : angle       0.75746 (13262)
  SS BOND              : bond        0.00234 (    9)
  SS BOND              : angle       2.85163 (   18)
  hydrogen bonds       : bond        0.06059 (  456)
  hydrogen bonds       : angle       5.23567 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 105
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6355 (mm-40)
REVERT: A  216 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.5973 (mmtm)
REVERT: A  392 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7754 (mt-10)
REVERT: B   46 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7621 (mtt-85)
REVERT: B   59 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7924 (m-80)
REVERT: N   83 MET cc_start: 0.7061 (mtp) cc_final: 0.6783 (mtm)
REVERT: N  120 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7437 (mp10)
REVERT: E   62 PHE cc_start: 0.2141 (OUTLIER) cc_final: 0.1449 (p90)
REVERT: E   71 ASN cc_start: 0.2468 (OUTLIER) cc_final: 0.1983 (m-40)
REVERT: E   75 MET cc_start: 0.2604 (OUTLIER) cc_final: 0.2176 (mpm)
REVERT: E  140 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5411 (mmm160)
REVERT: P   18 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7459 (tp40)
REVERT: R  177 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7595 (m-70)
REVERT: R  333 LYS cc_start: 0.5296 (mttp) cc_final: 0.4808 (mtpp)
REVERT: R  369 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.5416 (mmt)
REVERT: R  375 PHE cc_start: 0.7174 (m-10) cc_final: 0.6596 (m-80)
REVERT: R  390 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5830 (mt-10)
  outliers start: 62
  outliers final: 25
  residues processed: 149
  average time/residue: 0.6468
  time to fit residues: 102.5126
Evaluate side-chains
  130 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   71 ASN
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   15 CYS
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue  136 LYS
Chi-restraints excluded: chain R residue  177 HIS
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  314 ARG
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Chi-restraints excluded: chain R residue  390 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    0.0060
   chunk 80 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 266 HIS
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.215873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.166764 restraints weight = 9770.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.48
r_work: 0.3696 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9789  Z= 0.134
  Angle     :  0.584   7.168  13280  Z= 0.311
  Chirality :  0.043   0.147   1475
  Planarity :  0.004   0.045   1684
  Dihedral  :  5.207  32.629   1299
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 26.58 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1169
  helix:  1.19 (0.25), residues: 434
  sheet: -0.30 (0.32), residues: 236
  loop : -1.13 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 265 
 TYR   0.009   0.001   TYR N  95 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.023   0.002   TRP E 139 
 HIS   0.009   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9780)
  covalent geometry    : angle       0.58163 (13262)
  SS BOND              : bond        0.00192 (    9)
  SS BOND              : angle       1.65766 (   18)
  hydrogen bonds       : bond        0.04607 (  456)
  hydrogen bonds       : angle       4.82661 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6300 (mm-40)
REVERT: A  209 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6798 (mt-10)
REVERT: A  216 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6166 (mmtm)
REVERT: A  264 ASN cc_start: 0.5031 (OUTLIER) cc_final: 0.4823 (t0)
REVERT: A  392 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7819 (mt-10)
REVERT: B   59 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7969 (m-80)
REVERT: B  146 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8329 (mm)
REVERT: B  266 HIS cc_start: 0.7402 (t-90) cc_final: 0.6910 (t70)
REVERT: N   83 MET cc_start: 0.6981 (mtp) cc_final: 0.6672 (mtm)
REVERT: E   62 PHE cc_start: 0.2170 (OUTLIER) cc_final: 0.1498 (p90)
REVERT: E   75 MET cc_start: 0.2798 (OUTLIER) cc_final: 0.1584 (tmm)
REVERT: E  140 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4281 (mmm160)
REVERT: P   18 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7128 (tp40)
REVERT: R  287 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7376 (m-30)
REVERT: R  333 LYS cc_start: 0.5145 (mttp) cc_final: 0.4716 (mtpp)
REVERT: R  390 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5806 (mt-10)
  outliers start: 39
  outliers final: 17
  residues processed: 137
  average time/residue: 0.6730
  time to fit residues: 97.7030
Evaluate side-chains
  131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  314 ARG
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Chi-restraints excluded: chain R residue  390 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 176 GLN
E  86 ASN
E  97 HIS
R  50 GLN
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.215547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.171202 restraints weight = 9744.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 1.44
r_work: 0.3746 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9789  Z= 0.133
  Angle     :  0.582   7.069  13280  Z= 0.308
  Chirality :  0.043   0.147   1475
  Planarity :  0.004   0.045   1684
  Dihedral  :  5.086  30.897   1299
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.39 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.25), residues: 1169
  helix:  1.31 (0.25), residues: 434
  sheet: -0.28 (0.32), residues: 241
  loop : -1.04 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.008   0.001   TYR R 227 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.028   0.002   TRP E 139 
 HIS   0.008   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9780)
  covalent geometry    : angle       0.57947 (13262)
  SS BOND              : bond        0.00258 (    9)
  SS BOND              : angle       1.64000 (   18)
  hydrogen bonds       : bond        0.04507 (  456)
  hydrogen bonds       : angle       4.71658 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 106
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6313 (mm-40)
REVERT: A  216 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6137 (mmtm)
REVERT: A  264 ASN cc_start: 0.4932 (OUTLIER) cc_final: 0.4710 (t0)
REVERT: A  392 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7653 (mt-10)
REVERT: B   59 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7930 (m-80)
REVERT: B  146 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: B  266 HIS cc_start: 0.7482 (t-90) cc_final: 0.7085 (t70)
REVERT: G   29 LYS cc_start: 0.5552 (mtpp) cc_final: 0.5349 (mtpp)
REVERT: N   83 MET cc_start: 0.6873 (mtp) cc_final: 0.6585 (mtm)
REVERT: E   62 PHE cc_start: 0.2204 (OUTLIER) cc_final: 0.1559 (p90)
REVERT: E   75 MET cc_start: 0.2764 (OUTLIER) cc_final: 0.1623 (tmm)
REVERT: E  140 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.4231 (mmm160)
REVERT: P   18 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7109 (tp40)
REVERT: R  287 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7301 (m-30)
REVERT: R  333 LYS cc_start: 0.5118 (mttp) cc_final: 0.4733 (mtpp)
REVERT: R  339 LEU cc_start: 0.7455 (mp) cc_final: 0.7149 (mm)
REVERT: R  390 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5823 (mt-10)
  outliers start: 40
  outliers final: 22
  residues processed: 137
  average time/residue: 0.6884
  time to fit residues: 99.9434
Evaluate side-chains
  133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  314 ARG
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Chi-restraints excluded: chain R residue  390 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 176 GLN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** 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 = 0.4369 r_free = 0.4369 target = 0.215663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.172011 restraints weight = 9688.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 1.43
r_work: 0.3747 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3653 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9789  Z= 0.131
  Angle     :  0.581   7.115  13280  Z= 0.307
  Chirality :  0.043   0.161   1475
  Planarity :  0.004   0.045   1684
  Dihedral  :  5.036  30.150   1299
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.39 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.25), residues: 1169
  helix:  1.39 (0.25), residues: 433
  sheet: -0.27 (0.32), residues: 241
  loop : -1.03 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.007   0.001   TYR R 227 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.031   0.002   TRP E 139 
 HIS   0.011   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9780)
  covalent geometry    : angle       0.57841 (13262)
  SS BOND              : bond        0.00204 (    9)
  SS BOND              : angle       1.65504 (   18)
  hydrogen bonds       : bond        0.04424 (  456)
  hydrogen bonds       : angle       4.67473 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 104
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6331 (mm-40)
REVERT: A  216 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6150 (mmtm)
REVERT: B   46 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7319 (mmt-90)
REVERT: B   59 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7926 (m-80)
REVERT: B  146 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8289 (mm)
REVERT: B  266 HIS cc_start: 0.7481 (t-90) cc_final: 0.7028 (t70)
REVERT: G   29 LYS cc_start: 0.5714 (mtpp) cc_final: 0.5492 (mtpp)
REVERT: N   83 MET cc_start: 0.6867 (mtp) cc_final: 0.6566 (mtm)
REVERT: E   75 MET cc_start: 0.2740 (OUTLIER) cc_final: 0.1597 (tmm)
REVERT: E  140 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4269 (mmm160)
REVERT: P   18 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7217 (mp10)
REVERT: R  287 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7282 (m-30)
REVERT: R  333 LYS cc_start: 0.5204 (mttp) cc_final: 0.4803 (mtpp)
REVERT: R  339 LEU cc_start: 0.7456 (mp) cc_final: 0.7144 (mm)
REVERT: R  369 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.5102 (mmt)
REVERT: R  390 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5823 (mt-10)
  outliers start: 40
  outliers final: 22
  residues processed: 137
  average time/residue: 0.6663
  time to fit residues: 96.9009
Evaluate side-chains
  133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   15 CYS
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   68 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Chi-restraints excluded: chain R residue  390 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 28 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:    0.2980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 176 GLN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 374 HIS ** 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 = 0.4372 r_free = 0.4372 target = 0.216073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.171401 restraints weight = 9743.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 1.48
r_work: 0.3740 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9789  Z= 0.126
  Angle     :  0.572   7.303  13280  Z= 0.302
  Chirality :  0.043   0.169   1475
  Planarity :  0.004   0.051   1684
  Dihedral  :  4.968  29.504   1299
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 26.58 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.25), residues: 1169
  helix:  1.43 (0.25), residues: 433
  sheet: -0.27 (0.32), residues: 241
  loop : -0.99 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 265 
 TYR   0.007   0.001   TYR R 227 
 PHE   0.022   0.001   PHE R 257 
 TRP   0.033   0.002   TRP E 139 
 HIS   0.011   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9780)
  covalent geometry    : angle       0.56981 (13262)
  SS BOND              : bond        0.00201 (    9)
  SS BOND              : angle       1.55070 (   18)
  hydrogen bonds       : bond        0.04322 (  456)
  hydrogen bonds       : angle       4.62484 ( 1293)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6333 (mm-40)
REVERT: A  216 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6137 (mmtm)
REVERT: A  264 ASN cc_start: 0.4810 (OUTLIER) cc_final: 0.4596 (t0)
REVERT: A  392 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7605 (mt-10)
REVERT: B   46 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7317 (mmt-90)
REVERT: B   59 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7930 (m-80)
REVERT: B  146 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8282 (mm)
REVERT: B  215 GLU cc_start: 0.6484 (tt0) cc_final: 0.5997 (tt0)
REVERT: B  217 MET cc_start: 0.7278 (mtt) cc_final: 0.6923 (mtt)
REVERT: B  266 HIS cc_start: 0.7425 (t-90) cc_final: 0.6959 (t70)
REVERT: G   29 LYS cc_start: 0.5744 (mtpp) cc_final: 0.5530 (mtpp)
REVERT: N   83 MET cc_start: 0.6882 (mtp) cc_final: 0.6564 (mtm)
REVERT: E   75 MET cc_start: 0.2745 (OUTLIER) cc_final: 0.1596 (tmm)
REVERT: E  118 VAL cc_start: 0.5824 (m) cc_final: 0.5425 (p)
REVERT: E  133 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5950 (ttt)
REVERT: E  140 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.4303 (mmm160)
REVERT: P   18 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7262 (mp10)
REVERT: R  287 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7316 (m-30)
REVERT: R  333 LYS cc_start: 0.5210 (mttp) cc_final: 0.4831 (mtpp)
REVERT: R  369 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.5090 (mmt)
  outliers start: 35
  outliers final: 20
  residues processed: 133
  average time/residue: 0.6859
  time to fit residues: 96.7718
Evaluate side-chains
  132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue  112 SER
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain E residue   62 PHE
Chi-restraints excluded: chain E residue   75 MET
Chi-restraints excluded: chain E residue   79 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue   88 LEU
Chi-restraints excluded: chain E residue  105 THR
Chi-restraints excluded: chain E residue  133 MET
Chi-restraints excluded: chain E residue  140 ARG
Chi-restraints excluded: chain P residue    8 VAL
Chi-restraints excluded: chain P residue   15 CYS
Chi-restraints excluded: chain P residue   18 GLN
Chi-restraints excluded: chain P residue   39 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   82 THR
Chi-restraints excluded: chain R residue   84 SER
Chi-restraints excluded: chain R residue  287 ASP
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  338 THR
Chi-restraints excluded: chain R residue  351 LEU
Chi-restraints excluded: chain R residue  369 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 21 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 264 ASN
A 357 HIS
B 176 GLN
E  86 ASN
** E  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 200 ASN
** R 374 HIS ** 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 = 0.4361 r_free = 0.4361 target = 0.215119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.164630 restraints weight = 9712.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 1.45
r_work: 0.3726 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9789  Z= 0.159
  Angle     :  0.618   7.339  13280  Z= 0.327
  Chirality :  0.045   0.202   1475
  Planarity :  0.005   0.072   1684
  Dihedral  :  5.175  29.560   1299
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.97 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.25), residues: 1169
  helix:  1.33 (0.25), residues: 433
  sheet: -0.33 (0.32), residues: 243
  loop : -0.97 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 265 
 TYR   0.009   0.001   TYR N  32 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.034   0.002   TRP E 139 
 HIS   0.010   0.001   HIS E  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9780)
  covalent geometry    : angle       0.61483 (13262)
  SS BOND              : bond        0.00225 (    9)
  SS BOND              : angle       1.88417 (   18)
  hydrogen bonds       : bond        0.04699 (  456)
  hydrogen bonds       : angle       4.73787 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5268.15 seconds
wall clock time: 89 minutes 56.97 seconds (5396.97 seconds total)