Starting phenix.real_space_refine
on Sat Oct 11 14:43:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irv_35687/10_2025/8irv_35687.map"
  }
  resolution = 3.1
  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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4887      2.51       5
     N    1266      2.21       5
     O    1340      1.98       5
     H    7182      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14729
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 3924
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5107
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 4493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 4493
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 9, 'TRANS': 269}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 320
          Unusual residues: {'CLR': 10, 'PLM': 1, 'R5F': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 2.96, per 1000 atoms: 0.20
  Number of scatterers: 14729
  At special positions: 0
  Unit cell: (91.035, 101.745, 115.668, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     O    1340      8.00
     N    1266      7.00
     C    4887      6.00
     H    7182      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 113 " - pdb=" SG  CYS R 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 322 " - pdb=" SG  CYS R 335 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.36
  Conformation dependent library (CDL) restraints added in 363.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      51.0% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.958A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.646A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.508A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.456A  pdb=" N   GLN A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   GLU A 258 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.987A  pdb=" N   ARG A 273 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.964A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 321 through 340
      removed outlier: 3.670A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.528A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.858A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 25
      removed outlier: 3.644A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.507A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 38 through 68
      removed outlier: 3.622A  pdb=" N   VAL R  66 " --> pdb=" O   CYS R  62 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG R  67 " --> pdb=" O   ALA R  63 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER R  68 " --> pdb=" O   ALA R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 74
    Processing helix  chain 'R' and resid 75 through 94
      removed outlier: 4.155A  pdb=" N   PHE R  79 " --> pdb=" O   MET R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 105
      removed outlier: 3.562A  pdb=" N   LYS R  98 " --> pdb=" O   VAL R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 144
      removed outlier: 4.184A  pdb=" N   ASP R 114 " --> pdb=" O   GLY R 110 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL R 115 " --> pdb=" O   ALA R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 144 through 152
    Processing helix  chain 'R' and resid 153 through 178
      Proline residue:  R 175  - end of helix
    Processing helix  chain 'R' and resid 222 through 234
    Processing helix  chain 'R' and resid 234 through 271
    Processing helix  chain 'R' and resid 290 through 323
      removed outlier: 3.554A  pdb=" N   VAL R 294 " --> pdb=" O   LYS R 290 " (cutoff:3.500A)
      Proline residue:  R 311  - end of helix
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 337 through 361
      removed outlier: 3.753A  pdb=" N   SER R 352 " --> pdb=" O   GLY R 348 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER R 353 " --> pdb=" O   TRP R 349 " (cutoff:3.500A)
      Proline residue:  R 356  - end of helix
      removed outlier: 3.722A  pdb=" N   PHE R 361 " --> pdb=" O   VAL R 357 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 374
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.167A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.641A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.945A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.904A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.582A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.670A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.769A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.988A  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: 3.805A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.42

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 7155
        1.12 -     1.29: 1198
        1.29 -     1.47: 2781
        1.47 -     1.64: 3695
        1.64 -     1.82: 77
  Bond restraints: 14906
  Sorted by residual:
  bond pdb=" N   LYS R 296 "
       pdb=" H   LYS R 296 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR R 125 "
       pdb=" H   THR R 125 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" CE2 PHE B 234 "
       pdb=" HE2 PHE B 234 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CD1 TYR R 235 "
       pdb=" HD1 TYR R 235 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   GLY R 374 "
       pdb=" H   GLY R 374 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 14901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 22984
        2.73 -     5.46: 2917
        5.46 -     8.19: 779
        8.19 -    10.92: 16
       10.92 -    13.65: 27
  Bond angle restraints: 26723
  Sorted by residual:
  angle pdb=" CB  HIS B  54 "
        pdb=" CG  HIS B  54 "
        pdb=" CD2 HIS B  54 "
      ideal   model   delta    sigma   weight residual
     131.20  123.59    7.61 1.30e+00 5.92e-01 3.43e+01
  angle pdb=" N   ASP B 186 "
        pdb=" CA  ASP B 186 "
        pdb=" CB  ASP B 186 "
      ideal   model   delta    sigma   weight residual
     109.71  101.18    8.53 1.54e+00 4.22e-01 3.07e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" CB  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     109.69  101.40    8.29 1.53e+00 4.27e-01 2.94e+01
  angle pdb=" C   SER B 227 "
        pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     120.82  128.28   -7.46 1.41e+00 5.03e-01 2.80e+01
  angle pdb=" CB  HIS A 220 "
        pdb=" CG  HIS A 220 "
        pdb=" CD2 HIS A 220 "
      ideal   model   delta    sigma   weight residual
     131.20  124.38    6.82 1.30e+00 5.92e-01 2.75e+01
  ... (remaining 26718 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6960
       17.39 -    34.79: 387
       34.79 -    52.18: 93
       52.18 -    69.57: 84
       69.57 -    86.96: 4
  Dihedral angle restraints: 7528
    sinusoidal: 4355
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.93   28.07     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  LEU B   4 "
           pdb=" C   LEU B   4 "
           pdb=" N   ASP B   5 "
           pdb=" CA  ASP B   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.00  -28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LEU B  70 "
           pdb=" C   LEU B  70 "
           pdb=" N   VAL B  71 "
           pdb=" CA  VAL B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.05   26.95     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 7525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 866
       0.096 -    0.192: 288
       0.192 -    0.289: 44
       0.289 -    0.385: 14
       0.385 -    0.481: 4
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  SER B 334 "
            pdb=" N   SER B 334 "
            pdb=" C   SER B 334 "
            pdb=" CB  SER B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.78e+00
  chirality pdb=" CA  THR B  87 "
            pdb=" N   THR B  87 "
            pdb=" C   THR B  87 "
            pdb=" CB  THR B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.05    0.47 2.00e-01 2.50e+01 5.56e+00
  chirality pdb=" CA  TYR R 359 "
            pdb=" N   TYR R 359 "
            pdb=" C   TYR R 359 "
            pdb=" CB  TYR R 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.42 2.00e-01 2.50e+01 4.31e+00
  ... (remaining 1213 not shown)

  Planarity restraints: 2150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.211 2.00e-02 2.50e+03   8.32e-02 2.08e+02
        pdb=" CG  TYR B 105 "   -0.135 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "   -0.085 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.085 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 105 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 105 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 105 "    0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 271 "    0.162 2.00e-02 2.50e+03   7.19e-02 2.07e+02
        pdb=" CG  TRP A 271 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 271 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 271 "   -0.071 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 271 "   -0.061 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 271 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 271 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 271 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 271 "   -0.016 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 271 "    0.044 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 271 "    0.082 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 271 "   -0.100 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 271 "   -0.086 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 271 "    0.048 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 271 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 271 "    0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  54 "    0.141 2.00e-02 2.50e+03   8.21e-02 1.52e+02
        pdb=" CG  HIS B  54 "   -0.075 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  54 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  54 "   -0.101 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  54 "   -0.035 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  54 "   -0.053 2.00e-02 2.50e+03
        pdb=" HD2 HIS B  54 "   -0.016 2.00e-02 2.50e+03
        pdb=" HE1 HIS B  54 "    0.044 2.00e-02 2.50e+03
        pdb=" HE2 HIS B  54 "    0.132 2.00e-02 2.50e+03
  ... (remaining 2147 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 857
        2.18 -     2.79: 25538
        2.79 -     3.39: 41104
        3.39 -     4.00: 55614
        4.00 -     4.60: 80491
  Nonbonded interactions: 203604
  Sorted by model distance:
  nonbonded pdb=" HG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     1.576 2.450
  nonbonded pdb=" HH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" HG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OD1 ASP R 218 "
            pdb=" HG  SER R 220 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" HG  SER A  13 "
            pdb=" OD2 ASP A  16 "
     model   vdw
     1.602 2.450
  ... (remaining 203599 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.100
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.013   0.049   7726  Z= 0.756
  Angle     :  1.757   8.799  10522  Z= 1.183
  Chirality :  0.098   0.481   1216
  Planarity :  0.016   0.127   1270
  Dihedral  : 11.469  86.963   3347
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 0.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.46 %
  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 aren not related in a simple way.
  whole:  0.29 (0.26), residues: 896
  helix:  0.10 (0.22), residues: 412
  sheet:  1.02 (0.43), residues: 142
  loop :  0.17 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 314 
 TYR   0.199   0.020   TYR B 105 
 PHE   0.110   0.014   PHE R 312 
 TRP   0.118   0.023   TRP A 271 
 HIS   0.014   0.004   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.01257 ( 7724)
  covalent geometry    : angle       1.75739 (10518)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.66361 (    4)
  hydrogen bonds       : bond        0.17082 (  407)
  hydrogen bonds       : angle       6.77671 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8657 (tp) cc_final: 0.8438 (mt)
REVERT: A  329 TYR cc_start: 0.8706 (m-80) cc_final: 0.8439 (m-80)
REVERT: R  156 MET cc_start: 0.8286 (tpp) cc_final: 0.8064 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2930
  time to fit residues: 83.0544
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
B 132 ASN
B 237 ASN
B 239 ASN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.138179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.100231 restraints weight = 27917.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.58
r_work: 0.3010 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7726  Z= 0.153
  Angle     :  0.601   5.020  10522  Z= 0.333
  Chirality :  0.041   0.159   1216
  Planarity :  0.005   0.047   1270
  Dihedral  :  6.313  49.341   1677
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  6.85 %
    Favored  : 91.37 %
  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 aren not related in a simple way.
  whole:  1.12 (0.27), residues: 896
  helix:  1.27 (0.23), residues: 412
  sheet:  0.34 (0.37), residues: 172
  loop :  0.48 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.032   0.001   TYR B 105 
 PHE   0.022   0.002   PHE R 312 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7724)
  covalent geometry    : angle       0.60104 (10518)
  SS BOND              : bond        0.00068 (    2)
  SS BOND              : angle       1.25762 (    4)
  hydrogen bonds       : bond        0.06204 (  407)
  hydrogen bonds       : angle       5.01457 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8940 (tp) cc_final: 0.8634 (mt)
REVERT: A  320 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6717 (tt0)
REVERT: A  329 TYR cc_start: 0.8657 (m-80) cc_final: 0.8240 (m-80)
REVERT: B   12 GLU cc_start: 0.8416 (tp30) cc_final: 0.8136 (tp30)
REVERT: R   77 ASN cc_start: 0.8058 (m-40) cc_final: 0.7846 (m-40)
REVERT: R  180 TRP cc_start: 0.8937 (m-10) cc_final: 0.8517 (m-10)
  outliers start: 14
  outliers final: 7
  residues processed: 158
  average time/residue: 0.2504
  time to fit residues: 50.8526
Evaluate side-chains
  140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  318 MET
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.135664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.096689 restraints weight = 28499.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.65
r_work: 0.2954 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7726  Z= 0.180
  Angle     :  0.561   7.916  10522  Z= 0.309
  Chirality :  0.040   0.145   1216
  Planarity :  0.004   0.040   1270
  Dihedral  :  5.839  46.903   1677
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.14 %
    Favored  : 88.71 %
  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 aren not related in a simple way.
  whole:  1.35 (0.27), residues: 896
  helix:  1.69 (0.24), residues: 410
  sheet:  0.14 (0.37), residues: 170
  loop :  0.44 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.025   0.001   TYR B 105 
 PHE   0.020   0.002   PHE R 312 
 TRP   0.012   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 7724)
  covalent geometry    : angle       0.55388 (10518)
  SS BOND              : bond        0.00452 (    2)
  SS BOND              : angle       4.61138 (    4)
  hydrogen bonds       : bond        0.05645 (  407)
  hydrogen bonds       : angle       4.73779 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8966 (tp) cc_final: 0.8672 (mt)
REVERT: A  329 TYR cc_start: 0.8689 (m-80) cc_final: 0.8236 (m-80)
REVERT: B   16 ASN cc_start: 0.8539 (m-40) cc_final: 0.8192 (m110)
REVERT: B  134 ARG cc_start: 0.8205 (ptt180) cc_final: 0.7719 (ptm-80)
REVERT: R  180 TRP cc_start: 0.8881 (m-10) cc_final: 0.8461 (m-10)
REVERT: R  218 ASP cc_start: 0.7975 (t0) cc_final: 0.7703 (t70)
  outliers start: 17
  outliers final: 12
  residues processed: 156
  average time/residue: 0.2381
  time to fit residues: 48.5181
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  135 SER
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  171 ILE
Chi-restraints excluded: chain R residue  228 SER
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  345 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0050
   chunk 58 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0570
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4312

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.139308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.100405 restraints weight = 27996.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.65
r_work: 0.3037 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7726  Z= 0.105
  Angle     :  0.479   4.730  10522  Z= 0.262
  Chirality :  0.038   0.157   1216
  Planarity :  0.003   0.046   1270
  Dihedral  :  5.113  52.599   1677
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.04 %
    Favored  : 87.44 %
  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 aren not related in a simple way.
  whole:  1.48 (0.27), residues: 896
  helix:  2.01 (0.25), residues: 411
  sheet:  0.01 (0.36), residues: 167
  loop :  0.30 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.012   0.001   PHE R 312 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 7724)
  covalent geometry    : angle       0.47576 (10518)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       2.70982 (    4)
  hydrogen bonds       : bond        0.04608 (  407)
  hydrogen bonds       : angle       4.39106 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8966 (tp) cc_final: 0.8671 (mt)
REVERT: A  329 TYR cc_start: 0.8553 (m-80) cc_final: 0.8110 (m-80)
REVERT: B  134 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7769 (ptm-80)
REVERT: B  234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.7780 (m-80)
REVERT: B  291 ASP cc_start: 0.7860 (t0) cc_final: 0.7629 (t70)
REVERT: R  156 MET cc_start: 0.8107 (tpt) cc_final: 0.7852 (tpt)
REVERT: R  180 TRP cc_start: 0.8858 (m-10) cc_final: 0.8464 (m-10)
  outliers start: 12
  outliers final: 5
  residues processed: 148
  average time/residue: 0.2562
  time to fit residues: 48.5444
Evaluate side-chains
  139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain R residue   92 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.134981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.097164 restraints weight = 28301.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.58
r_work: 0.2960 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7726  Z= 0.182
  Angle     :  0.511   5.424  10522  Z= 0.279
  Chirality :  0.039   0.177   1216
  Planarity :  0.003   0.039   1270
  Dihedral  :  5.382  58.231   1677
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.04 %
    Favored  : 87.18 %
  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 aren not related in a simple way.
  whole:  1.48 (0.28), residues: 896
  helix:  2.07 (0.25), residues: 411
  sheet: -0.22 (0.36), residues: 172
  loop :  0.38 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 197 
 TYR   0.014   0.001   TYR B 105 
 PHE   0.017   0.001   PHE R 312 
 TRP   0.018   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7724)
  covalent geometry    : angle       0.50998 (10518)
  SS BOND              : bond        0.00828 (    2)
  SS BOND              : angle       1.92333 (    4)
  hydrogen bonds       : bond        0.04971 (  407)
  hydrogen bonds       : angle       4.45652 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8956 (tp) cc_final: 0.8618 (mt)
REVERT: A  320 GLU cc_start: 0.7246 (tt0) cc_final: 0.6789 (tt0)
REVERT: A  329 TYR cc_start: 0.8573 (m-80) cc_final: 0.8188 (m-80)
REVERT: B  134 ARG cc_start: 0.8280 (ptt180) cc_final: 0.7812 (ptm-80)
REVERT: B  197 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7700 (mmm-85)
REVERT: B  234 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: B  291 ASP cc_start: 0.7839 (t0) cc_final: 0.7585 (t70)
REVERT: R  180 TRP cc_start: 0.8856 (m-10) cc_final: 0.8440 (m-10)
REVERT: R  250 ARG cc_start: 0.8264 (mtm110) cc_final: 0.7957 (mtp180)
  outliers start: 14
  outliers final: 7
  residues processed: 140
  average time/residue: 0.2984
  time to fit residues: 51.9803
Evaluate side-chains
  134 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 270 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.136525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.097870 restraints weight = 28232.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.64
r_work: 0.2988 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7726  Z= 0.122
  Angle     :  0.478   4.667  10522  Z= 0.261
  Chirality :  0.038   0.134   1216
  Planarity :  0.003   0.050   1270
  Dihedral  :  5.119  50.840   1677
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.55 %
    Favored  : 87.18 %
  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 aren not related in a simple way.
  whole:  1.54 (0.28), residues: 896
  helix:  2.09 (0.25), residues: 413
  sheet: -0.19 (0.37), residues: 164
  loop :  0.40 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  19 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.015   0.001   PHE R 312 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7724)
  covalent geometry    : angle       0.47749 (10518)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       1.15051 (    4)
  hydrogen bonds       : bond        0.04630 (  407)
  hydrogen bonds       : angle       4.33998 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8913 (tp) cc_final: 0.8585 (mt)
REVERT: A  329 TYR cc_start: 0.8512 (m-80) cc_final: 0.8132 (m-80)
REVERT: B  197 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7582 (mmt90)
REVERT: B  234 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.7689 (m-80)
REVERT: B  291 ASP cc_start: 0.7857 (t0) cc_final: 0.7625 (t70)
REVERT: R   67 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7624 (ttp80)
REVERT: R   75 MET cc_start: 0.7732 (tpp) cc_final: 0.7359 (tpp)
REVERT: R  180 TRP cc_start: 0.8842 (m-10) cc_final: 0.8427 (m-10)
REVERT: R  250 ARG cc_start: 0.8240 (mtm110) cc_final: 0.7942 (mtp180)
REVERT: R  371 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7721 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 141
  average time/residue: 0.2538
  time to fit residues: 45.7753
Evaluate side-chains
  136 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0870
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8960

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

Flipped N/Q/H residues before XYZ refinement:
R 270 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.137255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.098523 restraints weight = 28007.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.65
r_work: 0.2996 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7726  Z= 0.115
  Angle     :  0.477   5.553  10522  Z= 0.257
  Chirality :  0.038   0.137   1216
  Planarity :  0.003   0.052   1270
  Dihedral  :  4.965  43.930   1677
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.44 %
    Favored  : 86.42 %
  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 aren not related in a simple way.
  whole:  1.56 (0.28), residues: 896
  helix:  2.11 (0.25), residues: 413
  sheet: -0.11 (0.38), residues: 164
  loop :  0.35 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.009   0.001   TYR A 329 
 PHE   0.014   0.001   PHE R 312 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7724)
  covalent geometry    : angle       0.47653 (10518)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.28526 (    4)
  hydrogen bonds       : bond        0.04488 (  407)
  hydrogen bonds       : angle       4.30157 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8985 (tp) cc_final: 0.8623 (mt)
REVERT: A  329 TYR cc_start: 0.8526 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  197 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7605 (mmt90)
REVERT: B  234 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.7628 (m-80)
REVERT: B  291 ASP cc_start: 0.7849 (t0) cc_final: 0.7579 (t70)
REVERT: R  180 TRP cc_start: 0.8845 (m-10) cc_final: 0.8450 (m-10)
REVERT: R  250 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7960 (mtp180)
  outliers start: 9
  outliers final: 7
  residues processed: 130
  average time/residue: 0.2718
  time to fit residues: 44.9384
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0270
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3842

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

Flipped N/Q/H residues before XYZ refinement:
** R 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 270 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.136096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.097467 restraints weight = 28558.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.65
r_work: 0.2979 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7726  Z= 0.140
  Angle     :  0.481   4.717  10522  Z= 0.261
  Chirality :  0.038   0.145   1216
  Planarity :  0.004   0.060   1270
  Dihedral  :  5.036  47.355   1677
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.56 %
    Favored  : 86.29 %
  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 aren not related in a simple way.
  whole:  1.56 (0.28), residues: 896
  helix:  2.06 (0.25), residues: 419
  sheet: -0.06 (0.38), residues: 164
  loop :  0.36 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.011   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 312 
 TRP   0.008   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7724)
  covalent geometry    : angle       0.48111 (10518)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       1.05518 (    4)
  hydrogen bonds       : bond        0.04614 (  407)
  hydrogen bonds       : angle       4.32942 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.9015 (tp) cc_final: 0.8650 (mt)
REVERT: A  286 LEU cc_start: 0.8759 (mp) cc_final: 0.8549 (mp)
REVERT: B  134 ARG cc_start: 0.8411 (ptt180) cc_final: 0.8059 (ptm-80)
REVERT: B  197 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7643 (mmt90)
REVERT: B  234 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.7706 (m-80)
REVERT: B  291 ASP cc_start: 0.7873 (t0) cc_final: 0.7599 (t70)
REVERT: R   75 MET cc_start: 0.7807 (tpp) cc_final: 0.7488 (tpp)
REVERT: R  180 TRP cc_start: 0.8850 (m-10) cc_final: 0.8468 (m-10)
REVERT: R  250 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7970 (mtp180)
  outliers start: 9
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2836
  time to fit residues: 47.7140
Evaluate side-chains
  135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  361 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** R 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 270 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.136222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.097325 restraints weight = 28412.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.65
r_work: 0.2985 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7726  Z= 0.139
  Angle     :  0.484   4.758  10522  Z= 0.262
  Chirality :  0.038   0.139   1216
  Planarity :  0.004   0.063   1270
  Dihedral  :  5.041  48.816   1677
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.07 %
    Favored  : 85.66 %
  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 aren not related in a simple way.
  whole:  1.54 (0.28), residues: 896
  helix:  2.07 (0.25), residues: 419
  sheet: -0.06 (0.38), residues: 164
  loop :  0.31 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  19 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 312 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7724)
  covalent geometry    : angle       0.48412 (10518)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.93950 (    4)
  hydrogen bonds       : bond        0.04567 (  407)
  hydrogen bonds       : angle       4.30871 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.9023 (tp) cc_final: 0.8643 (mt)
REVERT: A  286 LEU cc_start: 0.8764 (mp) cc_final: 0.8552 (mp)
REVERT: B  197 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7676 (mmt90)
REVERT: B  234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.7725 (m-80)
REVERT: B  291 ASP cc_start: 0.7859 (t0) cc_final: 0.7583 (t70)
REVERT: R   67 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7561 (ttp80)
REVERT: R   75 MET cc_start: 0.7782 (tpp) cc_final: 0.7443 (tpp)
REVERT: R  180 TRP cc_start: 0.8849 (m-10) cc_final: 0.8465 (m-10)
REVERT: R  250 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7950 (mtp180)
  outliers start: 10
  outliers final: 9
  residues processed: 131
  average time/residue: 0.2766
  time to fit residues: 45.5057
Evaluate side-chains
  135 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  166 THR
Chi-restraints excluded: chain R residue  361 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 5 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 230 ASN
R 270 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.137646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.098959 restraints weight = 28112.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.65
r_work: 0.2997 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.5175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7726  Z= 0.107
  Angle     :  0.464   4.719  10522  Z= 0.250
  Chirality :  0.038   0.140   1216
  Planarity :  0.004   0.068   1270
  Dihedral  :  4.838  48.354   1677
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.94 %
    Favored  : 85.91 %
  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 aren not related in a simple way.
  whole:  1.70 (0.28), residues: 896
  helix:  2.20 (0.25), residues: 419
  sheet:  0.02 (0.39), residues: 162
  loop :  0.38 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B  19 
 TYR   0.007   0.001   TYR B 105 
 PHE   0.013   0.001   PHE R 312 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7724)
  covalent geometry    : angle       0.46349 (10518)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.75482 (    4)
  hydrogen bonds       : bond        0.04312 (  407)
  hydrogen bonds       : angle       4.22370 ( 1185)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.9025 (tp) cc_final: 0.8652 (mt)
REVERT: A  286 LEU cc_start: 0.8765 (mp) cc_final: 0.8529 (mp)
REVERT: B  197 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7683 (mmt90)
REVERT: B  234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.7709 (m-80)
REVERT: B  291 ASP cc_start: 0.7849 (t0) cc_final: 0.7521 (t70)
REVERT: R   67 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7572 (ttp80)
REVERT: R   75 MET cc_start: 0.7799 (tpp) cc_final: 0.7459 (tpp)
REVERT: R  180 TRP cc_start: 0.8834 (m-10) cc_final: 0.8463 (m-10)
REVERT: R  250 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7950 (mtp180)
  outliers start: 9
  outliers final: 8
  residues processed: 133
  average time/residue: 0.2804
  time to fit residues: 47.1694
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  113 CYS
Chi-restraints excluded: chain R residue  137 ASP
Chi-restraints excluded: chain R residue  361 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
R 270 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.135871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.097060 restraints weight = 28147.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.64
r_work: 0.2965 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7726  Z= 0.161
  Angle     :  0.496   6.813  10522  Z= 0.268
  Chirality :  0.038   0.146   1216
  Planarity :  0.004   0.067   1270
  Dihedral  :  5.087  51.218   1677
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.20 %
    Favored  : 85.53 %
  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 aren not related in a simple way.
  whole:  1.67 (0.28), residues: 896
  helix:  2.18 (0.25), residues: 419
  sheet: -0.03 (0.38), residues: 162
  loop :  0.40 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  19 
 TYR   0.011   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 312 
 TRP   0.008   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7724)
  covalent geometry    : angle       0.49558 (10518)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.91851 (    4)
  hydrogen bonds       : bond        0.04565 (  407)
  hydrogen bonds       : angle       4.30250 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4667.71 seconds
wall clock time: 79 minutes 44.67 seconds (4784.67 seconds total)