Starting phenix.real_space_refine
on Mon May 12 12:08:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3j_7039/05_2025/6b3j_7039.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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      54      5.16       5
     C    5758      2.51       5
     N    1560      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9034
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 3134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3134
          Classifications: {'peptide': 380}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 364}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "P"
      Number of atoms: 254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 254
          Classifications: {'peptide': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 31}
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1654
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 6, 'TRANS': 188}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2595
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    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}
  Time building chain proxies: 4.97, per 1000 atoms: 0.55
  Number of scatterers: 9034
  At special positions: 0
  Unit cell: (82.68, 177.02, 98.58, 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      54     16.00
     O    1662      8.00
     N    1560      7.00
     C    5758      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03
    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=2.02

  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: 2.11
  Conformation dependent library (CDL) restraints added in 999.1 milliseconds
  

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      44.3% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 53
    Processing helix  chain 'R' and resid 91 through 95
      removed outlier: 3.577A  pdb=" N   SER R  94 " --> pdb=" O   TRP R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 170
      removed outlier: 4.006A  pdb=" N   ARG R 170 " --> pdb=" O   LEU R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 205
      removed outlier: 3.535A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 205 through 211
    Processing helix  chain 'R' and resid 213 through 223
    Processing helix  chain 'R' and resid 225 through 257
      removed outlier: 3.722A  pdb=" N   PHE R 230 " --> pdb=" O   CYS R 226 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   LEU R 231 " --> pdb=" O   ARG R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 292
      Proline residue:  R 277  - end of helix
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 296 through 300
      removed outlier: 3.785A  pdb=" N   ARG R 299 " --> pdb=" O   CYS R 296 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 337
      removed outlier: 3.640A  pdb=" N   TRP R 306 " --> pdb=" O   ASN R 302 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 361 through 370
    Processing helix  chain 'R' and resid 372 through 376
      removed outlier: 3.612A  pdb=" N   ARG R 376 " --> pdb=" O   GLU R 373 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 379 through 405
      removed outlier: 4.307A  pdb=" N   LYS R 383 " --> pdb=" O   LEU R 379 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR R 402 " --> pdb=" O   VAL R 398 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 423
    Processing helix  chain 'P' and resid 2 through 31
    Processing helix  chain 'A' and resid 12 through 39
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.126A  pdb=" N   GLN A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 4.112A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.832A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.987A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.734A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.632A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (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 'N' and resid 28 through 32
      removed outlier: 3.759A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.532A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.584A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 84
      removed outlier: 4.107A  pdb=" N   VAL R  83 " --> pdb=" O   VAL R 100 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL R 100 " --> pdb=" O   VAL R  83 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.602A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.570A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.715A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.608A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.354A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.724A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.892A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.583A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.792A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 7.111A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 2.47 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: 2888
        1.34 -     1.46: 2116
        1.46 -     1.58: 4163
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 9240
  Sorted by residual:
  bond pdb=" CB  TRP B 169 "
       pdb=" CG  TRP B 169 "
    ideal  model  delta    sigma   weight residual
    1.498  1.442  0.056 3.10e-02 1.04e+03 3.30e+00
  bond pdb=" C   VAL R 276 "
       pdb=" N   PRO R 277 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 1.36e-02 5.41e+03 3.30e+00
  bond pdb=" N   LYS R 113 "
       pdb=" CA  LYS R 113 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.023 1.29e-02 6.01e+03 3.16e+00
  bond pdb=" N   ILE R 357 "
       pdb=" CA  ILE R 357 "
    ideal  model  delta    sigma   weight residual
    1.464  1.484 -0.020 1.23e-02 6.61e+03 2.53e+00
  bond pdb=" CB  MET P  15 "
       pdb=" CG  MET P  15 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.35e+00
  ... (remaining 9235 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 12250
        2.80 -     5.59: 242
        5.59 -     8.39: 19
        8.39 -    11.18: 12
       11.18 -    13.98: 1
  Bond angle restraints: 12524
  Sorted by residual:
  angle pdb=" C   LYS N  76 "
        pdb=" N   ASN N  77 "
        pdb=" CA  ASN N  77 "
      ideal   model   delta    sigma   weight residual
     121.54  132.25  -10.71 1.91e+00 2.74e-01 3.14e+01
  angle pdb=" C   ASP B  66 "
        pdb=" N   SER B  67 "
        pdb=" CA  SER B  67 "
      ideal   model   delta    sigma   weight residual
     121.54  130.29   -8.75 1.91e+00 2.74e-01 2.10e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  129.75   -8.21 1.91e+00 2.74e-01 1.85e+01
  angle pdb=" C   GLU A 330 "
        pdb=" N   ASP A 331 "
        pdb=" CA  ASP A 331 "
      ideal   model   delta    sigma   weight residual
     121.59  135.57  -13.98 3.54e+00 7.98e-02 1.56e+01
  angle pdb=" N   GLY R 168 "
        pdb=" CA  GLY R 168 "
        pdb=" C   GLY R 168 "
      ideal   model   delta    sigma   weight residual
     112.73  117.15   -4.42 1.20e+00 6.94e-01 1.35e+01
  ... (remaining 12519 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.66: 5186
       15.66 -    31.33: 216
       31.33 -    46.99: 52
       46.99 -    62.65: 3
       62.65 -    78.32: 7
  Dihedral angle restraints: 5464
    sinusoidal: 2178
      harmonic: 3286
  Sorted by residual:
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.32  -78.32     1      1.00e+01 1.00e-02 7.66e+01
  dihedral pdb=" CA  ALA R  57 "
           pdb=" C   ALA R  57 "
           pdb=" N   THR R  58 "
           pdb=" CA  THR R  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.49   35.51     0      5.00e+00 4.00e-02 5.04e+01
  dihedral pdb=" CA  SER R 261 "
           pdb=" C   SER R 261 "
           pdb=" N   GLU R 262 "
           pdb=" CA  GLU R 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.28  -24.72     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 5461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1068
       0.069 -    0.138: 264
       0.138 -    0.207: 37
       0.207 -    0.276: 5
       0.276 -    0.345: 2
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CB  VAL R 276 "
            pdb=" CA  VAL R 276 "
            pdb=" CG1 VAL R 276 "
            pdb=" CG2 VAL R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CB  ILE R 317 "
            pdb=" CA  ILE R 317 "
            pdb=" CG1 ILE R 317 "
            pdb=" CG2 ILE R 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 272 "    0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   ILE R 272 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   ILE R 272 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY R 273 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 360 "   -0.059 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO A 361 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.025 2.00e-02 2.50e+03   1.96e-02 7.65e+00
        pdb=" CG  TYR B 105 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1594 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1328
        2.76 -     3.30: 8363
        3.30 -     3.83: 14711
        3.83 -     4.37: 16344
        4.37 -     4.90: 29559
  Nonbonded interactions: 70305
  Sorted by model distance:
  nonbonded pdb=" OG1 THR N  91 "
            pdb=" O   VAL N 124 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR R 105 "
            pdb=" O   LEU R 109 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.300 3.040
  ... (remaining 70300 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:             0.570
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.630
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
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      :  0.007   0.075   9246  Z= 0.310
  Angle     :  1.005  13.976  12536  Z= 0.569
  Chirality :  0.061   0.345   1376
  Planarity :  0.007   0.089   1597
  Dihedral  :  9.888  77.618   3320
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.24), residues: 1105
  helix:  2.60 (0.22), residues: 451
  sheet:  0.58 (0.37), residues: 196
  loop : -2.12 (0.24), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP R  72 
 HIS   0.010   0.002   HIS R 171 
 PHE   0.026   0.003   PHE R 367 
 TYR   0.048   0.004   TYR B 105 
 ARG   0.010   0.001   ARG R  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15739 (  477)
  hydrogen bonds       : angle       6.42273 ( 1380)
  SS BOND              : bond        0.00582 (    6)
  SS BOND              : angle       2.08567 (   12)
  covalent geometry    : bond        0.00692 ( 9240)
  covalent geometry    : angle       1.00377 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4130 (p0) cc_final: 0.3885 (m-30)
REVERT: R  123 LEU cc_start: 0.4851 (pp) cc_final: 0.4611 (tp)
REVERT: R  127 GLU cc_start: 0.6915 (tp30) cc_final: 0.6556 (mt-10)
REVERT: R  182 ASN cc_start: 0.8973 (m-40) cc_final: 0.8719 (m110)
REVERT: R  211 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7910 (tt0)
REVERT: R  242 TYR cc_start: 0.8440 (m-80) cc_final: 0.8026 (m-80)
REVERT: R  305 TYR cc_start: 0.7486 (m-10) cc_final: 0.7153 (m-10)
REVERT: R  351 LYS cc_start: 0.8633 (tttt) cc_final: 0.8249 (mmtt)
REVERT: R  367 PHE cc_start: 0.8126 (m-80) cc_final: 0.7925 (m-10)
REVERT: R  370 VAL cc_start: 0.7561 (t) cc_final: 0.7265 (t)
REVERT: R  393 PHE cc_start: 0.8134 (m-10) cc_final: 0.7760 (m-10)
REVERT: R  404 PHE cc_start: 0.4434 (t80) cc_final: 0.3359 (m-80)
REVERT: R  408 GLU cc_start: 0.8503 (pt0) cc_final: 0.8124 (pt0)
REVERT: P   21 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8192 (mmm-85)
REVERT: A  286 SER cc_start: 0.9165 (m) cc_final: 0.8717 (p)
REVERT: B   23 LYS cc_start: 0.8236 (tttp) cc_final: 0.7512 (mmtt)
REVERT: B   46 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.6555 (mtp-110)
REVERT: B   71 VAL cc_start: 0.8702 (t) cc_final: 0.8438 (p)
REVERT: B   82 TRP cc_start: 0.8855 (m100) cc_final: 0.8629 (m100)
REVERT: B  111 TYR cc_start: 0.8655 (m-80) cc_final: 0.8453 (m-80)
REVERT: B  154 ASP cc_start: 0.7964 (m-30) cc_final: 0.7611 (t0)
REVERT: B  189 SER cc_start: 0.9163 (t) cc_final: 0.8883 (p)
REVERT: B  191 SER cc_start: 0.8693 (t) cc_final: 0.8425 (p)
REVERT: B  217 MET cc_start: 0.7812 (ptp) cc_final: 0.7320 (tpt)
REVERT: G   14 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7309 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.2847
  time to fit residues: 90.1145
Evaluate side-chains
  124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
R 115 ASN
R 263 GLN
R 407 ASN
P   5 ASN
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B 155 ASN
B 266 HIS
G  24 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.117594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.103819 restraints weight = 23067.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.42
r_work: 0.3665 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9246  Z= 0.140
  Angle     :  0.637   9.034  12536  Z= 0.342
  Chirality :  0.043   0.173   1376
  Planarity :  0.004   0.052   1597
  Dihedral  :  5.501  50.400   1233
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.44 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1105
  helix:  2.92 (0.23), residues: 451
  sheet:  0.46 (0.36), residues: 203
  loop : -1.73 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R  33 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.026   0.002   PHE R 230 
 TYR   0.018   0.002   TYR R 402 
 ARG   0.006   0.001   ARG R 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04585 (  477)
  hydrogen bonds       : angle       5.02461 ( 1380)
  SS BOND              : bond        0.00400 (    6)
  SS BOND              : angle       3.76414 (   12)
  covalent geometry    : bond        0.00303 ( 9240)
  covalent geometry    : angle       0.62686 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.046 
Fit side-chains
REVERT: R   67 ASP cc_start: 0.5032 (p0) cc_final: 0.4071 (m-30)
REVERT: R  305 TYR cc_start: 0.7438 (m-10) cc_final: 0.7209 (m-10)
REVERT: R  354 LEU cc_start: 0.8268 (mt) cc_final: 0.8041 (tt)
REVERT: R  404 PHE cc_start: 0.4595 (t80) cc_final: 0.3804 (m-80)
REVERT: A  318 TYR cc_start: 0.5979 (t80) cc_final: 0.5442 (t80)
REVERT: B   23 LYS cc_start: 0.8138 (tttp) cc_final: 0.7714 (mmtt)
REVERT: B   82 TRP cc_start: 0.8699 (m100) cc_final: 0.8366 (m100)
REVERT: B  270 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (pp)
REVERT: G   14 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7618 (tttp)
  outliers start: 18
  outliers final: 11
  residues processed: 154
  average time/residue: 0.2225
  time to fit residues: 47.1731
Evaluate side-chains
  128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   35 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.114391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.099799 restraints weight = 23505.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.81
r_work: 0.3584 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9246  Z= 0.177
  Angle     :  0.624   8.660  12536  Z= 0.334
  Chirality :  0.043   0.167   1376
  Planarity :  0.004   0.057   1597
  Dihedral  :  5.327  44.127   1233
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 10.30 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1105
  helix:  2.77 (0.23), residues: 451
  sheet:  0.34 (0.36), residues: 203
  loop : -1.58 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 243 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.028   0.002   PHE R 385 
 TYR   0.020   0.002   TYR R 402 
 ARG   0.005   0.001   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  477)
  hydrogen bonds       : angle       4.79615 ( 1380)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       3.14728 (   12)
  covalent geometry    : bond        0.00401 ( 9240)
  covalent geometry    : angle       0.61679 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4696 (p0) cc_final: 0.3888 (m-30)
REVERT: R  139 GLU cc_start: 0.7039 (tt0) cc_final: 0.6369 (pm20)
REVERT: R  298 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8033 (t)
REVERT: R  404 PHE cc_start: 0.4509 (t80) cc_final: 0.3731 (m-80)
REVERT: A   27 GLU cc_start: 0.7626 (pp20) cc_final: 0.7386 (pp20)
REVERT: A  318 TYR cc_start: 0.6072 (t80) cc_final: 0.5539 (t80)
REVERT: B   23 LYS cc_start: 0.8434 (tttp) cc_final: 0.7744 (mmtt)
REVERT: B   82 TRP cc_start: 0.8824 (m100) cc_final: 0.8594 (m100)
REVERT: G   14 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7506 (tttp)
  outliers start: 31
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1892
  time to fit residues: 39.0666
Evaluate side-chains
  128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 LEU
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain P residue    3 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   21 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0270
   chunk 61 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.116394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.102019 restraints weight = 23149.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.82
r_work: 0.3626 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9246  Z= 0.110
  Angle     :  0.544   6.973  12536  Z= 0.292
  Chirality :  0.040   0.153   1376
  Planarity :  0.004   0.052   1597
  Dihedral  :  4.943  39.113   1233
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.33 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1105
  helix:  2.93 (0.24), residues: 448
  sheet:  0.20 (0.36), residues: 201
  loop : -1.34 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 243 
 HIS   0.003   0.001   HIS R  99 
 PHE   0.020   0.001   PHE R 385 
 TYR   0.015   0.001   TYR N  60 
 ARG   0.006   0.000   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  477)
  hydrogen bonds       : angle       4.43277 ( 1380)
  SS BOND              : bond        0.00227 (    6)
  SS BOND              : angle       2.42334 (   12)
  covalent geometry    : bond        0.00231 ( 9240)
  covalent geometry    : angle       0.53945 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4455 (p0) cc_final: 0.4026 (m-30)
REVERT: R  139 GLU cc_start: 0.7127 (tt0) cc_final: 0.6420 (pm20)
REVERT: R  269 TYR cc_start: 0.8125 (m-80) cc_final: 0.7560 (m-80)
REVERT: R  298 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.7999 (t)
REVERT: R  404 PHE cc_start: 0.4443 (t80) cc_final: 0.3657 (m-80)
REVERT: A   27 GLU cc_start: 0.7546 (pp20) cc_final: 0.7308 (pp20)
REVERT: A  318 TYR cc_start: 0.5957 (t80) cc_final: 0.5432 (t80)
REVERT: B   23 LYS cc_start: 0.8376 (tttp) cc_final: 0.7770 (mmtt)
REVERT: B   45 MET cc_start: 0.8347 (mtp) cc_final: 0.8018 (mtp)
REVERT: B   82 TRP cc_start: 0.8808 (m100) cc_final: 0.8519 (m100)
REVERT: B  170 ASP cc_start: 0.7151 (t0) cc_final: 0.6915 (t0)
REVERT: B  270 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (pp)
REVERT: G   14 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7490 (tttp)
  outliers start: 23
  outliers final: 17
  residues processed: 136
  average time/residue: 0.1865
  time to fit residues: 36.6268
Evaluate side-chains
  127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain P residue    3 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R  99 HIS
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.116858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102546 restraints weight = 23295.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.85
r_work: 0.3632 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9246  Z= 0.105
  Angle     :  0.521   6.271  12536  Z= 0.278
  Chirality :  0.040   0.153   1376
  Planarity :  0.004   0.049   1597
  Dihedral  :  4.671  36.619   1233
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.15 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.26), residues: 1105
  helix:  2.94 (0.24), residues: 448
  sheet:  0.22 (0.36), residues: 201
  loop : -1.29 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 120 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 385 
 TYR   0.016   0.001   TYR R  69 
 ARG   0.006   0.000   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  477)
  hydrogen bonds       : angle       4.28052 ( 1380)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       2.25160 (   12)
  covalent geometry    : bond        0.00221 ( 9240)
  covalent geometry    : angle       0.51679 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4464 (p0) cc_final: 0.4037 (m-30)
REVERT: R  139 GLU cc_start: 0.7067 (tt0) cc_final: 0.6355 (pm20)
REVERT: R  247 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8056 (tp30)
REVERT: R  265 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7142 (mm)
REVERT: R  269 TYR cc_start: 0.8145 (m-80) cc_final: 0.7867 (m-80)
REVERT: R  367 PHE cc_start: 0.7967 (m-80) cc_final: 0.7756 (m-10)
REVERT: R  404 PHE cc_start: 0.4419 (t80) cc_final: 0.3718 (m-80)
REVERT: A   27 GLU cc_start: 0.7631 (pp20) cc_final: 0.7359 (pp20)
REVERT: A  318 TYR cc_start: 0.5972 (t80) cc_final: 0.5543 (t80)
REVERT: B   23 LYS cc_start: 0.8386 (tttp) cc_final: 0.7749 (mmtt)
REVERT: B   45 MET cc_start: 0.8316 (mtp) cc_final: 0.8064 (mtp)
REVERT: B   61 MET cc_start: 0.9049 (ppp) cc_final: 0.8848 (ptm)
REVERT: B   82 TRP cc_start: 0.8797 (m100) cc_final: 0.8503 (m100)
REVERT: B  170 ASP cc_start: 0.7171 (t0) cc_final: 0.6956 (t0)
REVERT: B  270 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8390 (pp)
REVERT: G   14 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7492 (tttp)
  outliers start: 26
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1871
  time to fit residues: 38.5945
Evaluate side-chains
  127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  265 ILE
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 78 optimal weight:    0.6980
   chunk 65 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
R  45 GLN
B 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.115751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.101251 restraints weight = 23227.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.83
r_work: 0.3609 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9246  Z= 0.128
  Angle     :  0.548   9.106  12536  Z= 0.290
  Chirality :  0.040   0.159   1376
  Planarity :  0.004   0.050   1597
  Dihedral  :  4.716  36.144   1233
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.49 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.26), residues: 1105
  helix:  2.85 (0.24), residues: 447
  sheet:  0.15 (0.35), residues: 203
  loop : -1.28 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 120 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.002   PHE R 385 
 TYR   0.015   0.001   TYR R 242 
 ARG   0.006   0.000   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  477)
  hydrogen bonds       : angle       4.29466 ( 1380)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       2.32079 (   12)
  covalent geometry    : bond        0.00286 ( 9240)
  covalent geometry    : angle       0.54390 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 1.066 
Fit side-chains
REVERT: R   67 ASP cc_start: 0.4435 (p0) cc_final: 0.3992 (m-30)
REVERT: R  139 GLU cc_start: 0.7174 (tt0) cc_final: 0.6419 (pm20)
REVERT: R  247 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8071 (tp30)
REVERT: R  265 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7086 (mm)
REVERT: R  269 TYR cc_start: 0.8184 (m-80) cc_final: 0.7867 (m-80)
REVERT: R  367 PHE cc_start: 0.8044 (m-80) cc_final: 0.7737 (m-10)
REVERT: R  400 ILE cc_start: 0.7989 (tt) cc_final: 0.7444 (mm)
REVERT: R  404 PHE cc_start: 0.4386 (t80) cc_final: 0.3646 (m-80)
REVERT: A   27 GLU cc_start: 0.7743 (pp20) cc_final: 0.7464 (pp20)
REVERT: A  318 TYR cc_start: 0.5985 (t80) cc_final: 0.5551 (t80)
REVERT: B   23 LYS cc_start: 0.8444 (tttp) cc_final: 0.7762 (mmtt)
REVERT: B   82 TRP cc_start: 0.8842 (m100) cc_final: 0.8549 (m100)
REVERT: B  170 ASP cc_start: 0.7254 (t0) cc_final: 0.7022 (t0)
REVERT: B  270 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8426 (pp)
REVERT: G   14 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7531 (tttp)
  outliers start: 29
  outliers final: 21
  residues processed: 135
  average time/residue: 0.1805
  time to fit residues: 35.6652
Evaluate side-chains
  131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  265 ILE
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   chunk 27 optimal weight:    0.4980
   chunk 82 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  88 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 = 0.3871 r_free = 0.3871 target = 0.111987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.097704 restraints weight = 24036.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.82
r_work: 0.3542 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9246  Z= 0.233
  Angle     :  0.657   9.953  12536  Z= 0.349
  Chirality :  0.044   0.177   1376
  Planarity :  0.004   0.047   1597
  Dihedral  :  5.216  37.724   1233
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.62 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.25), residues: 1105
  helix:  2.79 (0.24), residues: 436
  sheet: -0.17 (0.33), residues: 231
  loop : -1.52 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 110 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.024   0.002   PHE R 385 
 TYR   0.018   0.002   TYR R 291 
 ARG   0.007   0.001   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  477)
  hydrogen bonds       : angle       4.61327 ( 1380)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       2.79294 (   12)
  covalent geometry    : bond        0.00532 ( 9240)
  covalent geometry    : angle       0.65150 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4575 (p0) cc_final: 0.4032 (m-30)
REVERT: R  139 GLU cc_start: 0.7079 (tt0) cc_final: 0.6403 (pm20)
REVERT: R  247 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8153 (tp30)
REVERT: R  354 LEU cc_start: 0.8401 (mt) cc_final: 0.8155 (tt)
REVERT: R  367 PHE cc_start: 0.8340 (m-80) cc_final: 0.7977 (m-10)
REVERT: R  404 PHE cc_start: 0.4419 (t80) cc_final: 0.3677 (m-80)
REVERT: A   27 GLU cc_start: 0.7782 (pp20) cc_final: 0.7449 (pp20)
REVERT: A  318 TYR cc_start: 0.6115 (t80) cc_final: 0.5630 (t80)
REVERT: B   23 LYS cc_start: 0.8690 (tttp) cc_final: 0.7941 (mmtt)
REVERT: B   45 MET cc_start: 0.8303 (mtp) cc_final: 0.7975 (mtp)
REVERT: B   82 TRP cc_start: 0.8863 (m100) cc_final: 0.8630 (m100)
REVERT: B  234 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7680 (t80)
REVERT: G   14 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7495 (tttp)
REVERT: G   51 LEU cc_start: 0.7250 (tp) cc_final: 0.6974 (mt)
REVERT: N   21 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7770 (p)
  outliers start: 29
  outliers final: 20
  residues processed: 125
  average time/residue: 0.1808
  time to fit residues: 32.9859
Evaluate side-chains
  118 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 18 optimal weight:    0.4980
   chunk 45 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.114709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.100222 restraints weight = 23796.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.85
r_work: 0.3585 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9246  Z= 0.121
  Angle     :  0.565   7.106  12536  Z= 0.299
  Chirality :  0.041   0.156   1376
  Planarity :  0.004   0.047   1597
  Dihedral  :  4.867  36.237   1233
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.55 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1105
  helix:  2.85 (0.24), residues: 442
  sheet: -0.17 (0.33), residues: 227
  loop : -1.37 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 120 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE R 385 
 TYR   0.015   0.001   TYR R  69 
 ARG   0.002   0.000   ARG R  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  477)
  hydrogen bonds       : angle       4.34849 ( 1380)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       2.38238 (   12)
  covalent geometry    : bond        0.00265 ( 9240)
  covalent geometry    : angle       0.56018 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4233 (p0) cc_final: 0.3918 (m-30)
REVERT: R  139 GLU cc_start: 0.7142 (tt0) cc_final: 0.6471 (pm20)
REVERT: R  247 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8170 (tp30)
REVERT: R  269 TYR cc_start: 0.8459 (m-80) cc_final: 0.8148 (m-80)
REVERT: R  354 LEU cc_start: 0.8340 (mt) cc_final: 0.8088 (tt)
REVERT: R  367 PHE cc_start: 0.8253 (m-80) cc_final: 0.7974 (m-10)
REVERT: R  404 PHE cc_start: 0.4356 (t80) cc_final: 0.3658 (m-80)
REVERT: P   13 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8662 (mmmm)
REVERT: A   27 GLU cc_start: 0.7847 (pp20) cc_final: 0.7523 (pp20)
REVERT: A  318 TYR cc_start: 0.5879 (t80) cc_final: 0.5483 (t80)
REVERT: B   23 LYS cc_start: 0.8543 (tttp) cc_final: 0.7821 (mmtt)
REVERT: B   45 MET cc_start: 0.8287 (mtp) cc_final: 0.8021 (mtp)
REVERT: B   82 TRP cc_start: 0.8874 (m100) cc_final: 0.8645 (m100)
REVERT: B  234 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7588 (t80)
REVERT: B  270 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (pp)
REVERT: G   14 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7463 (tttp)
  outliers start: 25
  outliers final: 18
  residues processed: 130
  average time/residue: 0.1863
  time to fit residues: 35.6585
Evaluate side-chains
  123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0770
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5944

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.114613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.100078 restraints weight = 23466.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.83
r_work: 0.3586 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9246  Z= 0.135
  Angle     :  0.578   7.338  12536  Z= 0.304
  Chirality :  0.041   0.157   1376
  Planarity :  0.004   0.048   1597
  Dihedral  :  4.801  36.192   1233
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.96 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1105
  helix:  2.83 (0.24), residues: 443
  sheet: -0.08 (0.34), residues: 214
  loop : -1.32 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R  39 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.022   0.002   PHE R 385 
 TYR   0.014   0.002   TYR R  69 
 ARG   0.003   0.000   ARG R  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  477)
  hydrogen bonds       : angle       4.32515 ( 1380)
  SS BOND              : bond        0.00292 (    6)
  SS BOND              : angle       2.42616 (   12)
  covalent geometry    : bond        0.00302 ( 9240)
  covalent geometry    : angle       0.57364 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4255 (p0) cc_final: 0.3929 (m-30)
REVERT: R  139 GLU cc_start: 0.7116 (tt0) cc_final: 0.6478 (pm20)
REVERT: R  242 TYR cc_start: 0.8610 (m-80) cc_final: 0.8297 (m-80)
REVERT: R  247 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8092 (tp30)
REVERT: R  269 TYR cc_start: 0.8439 (m-80) cc_final: 0.8217 (m-80)
REVERT: R  354 LEU cc_start: 0.8379 (mt) cc_final: 0.8109 (tt)
REVERT: R  367 PHE cc_start: 0.8364 (m-80) cc_final: 0.8042 (m-10)
REVERT: R  400 ILE cc_start: 0.7902 (tt) cc_final: 0.7363 (mm)
REVERT: R  404 PHE cc_start: 0.4384 (t80) cc_final: 0.3692 (m-80)
REVERT: P   10 ASP cc_start: 0.8055 (t0) cc_final: 0.7824 (t0)
REVERT: A   27 GLU cc_start: 0.7851 (pp20) cc_final: 0.7514 (pp20)
REVERT: A  318 TYR cc_start: 0.5936 (t80) cc_final: 0.5552 (t80)
REVERT: B   23 LYS cc_start: 0.8572 (tttp) cc_final: 0.7811 (mmtt)
REVERT: B   45 MET cc_start: 0.8279 (mtp) cc_final: 0.7997 (mtp)
REVERT: B   82 TRP cc_start: 0.8848 (m100) cc_final: 0.8617 (m100)
REVERT: B  234 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7594 (t80)
REVERT: B  270 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8390 (pp)
REVERT: G   14 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7516 (tttp)
  outliers start: 24
  outliers final: 19
  residues processed: 126
  average time/residue: 0.1833
  time to fit residues: 33.6841
Evaluate side-chains
  127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.114568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.100024 restraints weight = 23540.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.84
r_work: 0.3585 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9246  Z= 0.140
  Angle     :  0.591   7.702  12536  Z= 0.309
  Chirality :  0.041   0.156   1376
  Planarity :  0.004   0.048   1597
  Dihedral  :  4.789  35.812   1233
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.86 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1105
  helix:  2.93 (0.24), residues: 437
  sheet: -0.21 (0.33), residues: 230
  loop : -1.34 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R  39 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.022   0.002   PHE R 385 
 TYR   0.013   0.002   TYR N  80 
 ARG   0.003   0.000   ARG R  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  477)
  hydrogen bonds       : angle       4.33247 ( 1380)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       2.45190 (   12)
  covalent geometry    : bond        0.00317 ( 9240)
  covalent geometry    : angle       0.58683 (12524)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   67 ASP cc_start: 0.4363 (p0) cc_final: 0.3921 (m-30)
REVERT: R  139 GLU cc_start: 0.7181 (tt0) cc_final: 0.6547 (pm20)
REVERT: R  247 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (tp30)
REVERT: R  354 LEU cc_start: 0.8469 (mt) cc_final: 0.8177 (tt)
REVERT: R  367 PHE cc_start: 0.8343 (m-80) cc_final: 0.8034 (m-10)
REVERT: R  400 ILE cc_start: 0.7855 (tt) cc_final: 0.7325 (mm)
REVERT: R  404 PHE cc_start: 0.4784 (t80) cc_final: 0.3848 (m-80)
REVERT: P   10 ASP cc_start: 0.8019 (t0) cc_final: 0.7806 (t0)
REVERT: A   27 GLU cc_start: 0.7852 (pp20) cc_final: 0.7519 (pp20)
REVERT: A  318 TYR cc_start: 0.5936 (t80) cc_final: 0.5561 (t80)
REVERT: B   23 LYS cc_start: 0.8580 (tttp) cc_final: 0.7816 (mmtt)
REVERT: B   45 MET cc_start: 0.8248 (mtp) cc_final: 0.7980 (mtp)
REVERT: B   82 TRP cc_start: 0.8847 (m100) cc_final: 0.8623 (m100)
REVERT: B  270 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8369 (pp)
REVERT: G   14 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7525 (tttp)
REVERT: N   21 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7727 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1845
  time to fit residues: 33.5619
Evaluate side-chains
  129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  201 LEU
Chi-restraints excluded: chain R residue  232 LEU
Chi-restraints excluded: chain R residue  247 GLU
Chi-restraints excluded: chain R residue  278 LEU
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  113 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4495 > 50:
  distance: 10 - 101:  12.898
  distance: 75 - 79:   8.850
  distance: 80 - 81:  11.689
  distance: 80 - 83:   4.567
  distance: 81 - 82:   5.613
  distance: 81 - 91:  15.776
  distance: 83 - 84:   3.928
  distance: 84 - 86:   8.057
  distance: 85 - 87:   3.426
  distance: 86 - 88:   5.495
  distance: 87 - 89:   8.076
  distance: 88 - 89:   4.081
  distance: 89 - 90:   4.539
  distance: 91 - 92:  11.133
  distance: 92 - 95:  20.671
  distance: 93 - 94:  14.966
  distance: 93 - 96:   8.383
  distance: 96 - 97:   3.726
  distance: 97 - 98:  15.868
  distance: 98 - 99:  12.568
  distance: 98 - 102:  13.871
  distance: 100 - 101:  10.058
  distance: 102 - 103:  22.187
  distance: 103 - 104:  13.865
  distance: 103 - 106:   7.731
  distance: 104 - 105:  15.080
  distance: 104 - 116:   7.030
  distance: 106 - 107:   4.255
  distance: 107 - 108:   4.366
  distance: 107 - 109:   4.310
  distance: 109 - 111:   3.564
  distance: 109 - 112:   3.006
  distance: 110 - 111:   3.388
  distance: 111 - 113:   4.593
  distance: 112 - 114:   6.828
  distance: 113 - 115:   5.648
  distance: 114 - 115:   6.161
  distance: 116 - 117:  32.219
  distance: 116 - 122:  22.892
  distance: 117 - 118:  13.768
  distance: 117 - 120:  29.745
  distance: 118 - 119:  16.333
  distance: 118 - 123:   5.324
  distance: 120 - 121:  17.667
  distance: 121 - 122:  24.174
  distance: 123 - 124:  25.301
  distance: 124 - 125:   8.581
  distance: 124 - 127:  12.992
  distance: 125 - 126:  34.465
  distance: 125 - 131:  20.435
  distance: 127 - 128:   3.242
  distance: 128 - 129:  12.220
  distance: 128 - 130:  11.982
  distance: 131 - 132:  28.445
  distance: 132 - 133:  11.830
  distance: 133 - 134:  16.525
  distance: 133 - 135:  12.193
  distance: 135 - 136:  13.079
  distance: 136 - 137:  14.886
  distance: 136 - 139:   7.633
  distance: 137 - 138:  24.313
  distance: 137 - 144:   8.378
  distance: 139 - 140:  12.862
  distance: 140 - 141:  12.175
  distance: 141 - 142:  13.965
  distance: 141 - 143:  18.226
  distance: 144 - 145:   8.856
  distance: 144 - 150:  11.182
  distance: 145 - 146:   6.354
  distance: 145 - 148:  12.962
  distance: 146 - 151:  17.178
  distance: 148 - 149:  17.840
  distance: 149 - 150:  10.731
  distance: 151 - 152:  10.389
  distance: 152 - 153:   6.330
  distance: 153 - 154:  11.664
  distance: 153 - 155:  14.453