Starting phenix.real_space_refine
on Thu May 15 11:33:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uoy_42441/05_2025/8uoy_42441.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4182      2.51       5
     N    1122      2.21       5
     O    1318      1.98       5
     H    6544      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 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: 13188
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 6594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6594
          Classifications: {'peptide': 436}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 424}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
  Time building chain proxies: 6.34, per 1000 atoms: 0.48
  Number of scatterers: 13188
  At special positions: 0
  Unit cell: (119.658, 76.538, 86.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     O    1318      8.00
     N    1122      7.00
     C    4182      6.00
     H    6544      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      43.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 3.562A  pdb=" N   ALA B  78 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 99
      removed outlier: 3.944A  pdb=" N   ALA B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 127
      removed outlier: 3.516A  pdb=" N   ALA B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 152 through 156
      removed outlier: 4.281A  pdb=" N   HIS B 155 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   SER B 156 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 152 through 156'
    Processing helix  chain 'B' and resid 174 through 179
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 183 through 197
      removed outlier: 3.660A  pdb=" N   HIS B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 4.156A  pdb=" N   ILE B 222 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 273 through 280
      removed outlier: 3.866A  pdb=" N   ASP B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 310
      removed outlier: 4.261A  pdb=" N   GLU B 308 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 335
    Processing helix  chain 'B' and resid 346 through 349
      removed outlier: 3.785A  pdb=" N   GLY B 349 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 346 through 349'
    Processing helix  chain 'B' and resid 350 through 364
    Processing helix  chain 'B' and resid 380 through 390
      removed outlier: 4.170A  pdb=" N   ALA B 386 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL B 387 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 406
    Processing helix  chain 'B' and resid 407 through 416
      removed outlier: 4.413A  pdb=" N   ARG B 413 " --> pdb=" O   ASN B 409 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 62
    Processing helix  chain 'C' and resid 64 through 79
      removed outlier: 5.887A  pdb=" N   ASN C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE C  74 " --> pdb=" O   ASN C  70 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA C  76 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU C  77 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA C  78 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 99
      removed outlier: 3.581A  pdb=" N   ILE C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 119
    Processing helix  chain 'C' and resid 122 through 127
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 153 through 156
      removed outlier: 3.521A  pdb=" N   SER C 156 " --> pdb=" O   GLY C 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 153 through 156'
    Processing helix  chain 'C' and resid 174 through 179
    Processing helix  chain 'C' and resid 184 through 197
      removed outlier: 3.953A  pdb=" N   ALA C 188 " --> pdb=" O   GLU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 229
      removed outlier: 3.936A  pdb=" N   VAL C 219 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU C 220 " --> pdb=" O   GLU C 216 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE C 222 " --> pdb=" O   GLY C 218 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LEU C 223 " --> pdb=" O   VAL C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 249
    Processing helix  chain 'C' and resid 260 through 262
      No H-bonds generated for 'chain 'C' and resid 260 through 262'
    Processing helix  chain 'C' and resid 271 through 280
      removed outlier: 3.507A  pdb=" N   GLU C 280 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 284
    Processing helix  chain 'C' and resid 299 through 311
      removed outlier: 4.415A  pdb=" N   THR C 307 " --> pdb=" O   TRP C 303 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLU C 308 " --> pdb=" O   LYS C 304 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ARG C 309 " --> pdb=" O   VAL C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 335
      removed outlier: 3.685A  pdb=" N   LYS C 334 " --> pdb=" O   ALA C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 348
      No H-bonds generated for 'chain 'C' and resid 346 through 348'
    Processing helix  chain 'C' and resid 350 through 365
      removed outlier: 3.705A  pdb=" N   ALA C 364 " --> pdb=" O   MET C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 385
      removed outlier: 3.690A  pdb=" N   ASP C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 401 through 409
      removed outlier: 4.674A  pdb=" N   LYS C 407 " --> pdb=" O   ASP C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 419
      removed outlier: 5.245A  pdb=" N   GLU C 415 " --> pdb=" O   LEU C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 420 through 422
      No H-bonds generated for 'chain 'C' and resid 420 through 422'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 14
      removed outlier: 4.036A  pdb=" N   ASP B   6 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL B  12 " --> pdb=" O   THR B  20 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN B  18 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145
      removed outlier: 6.252A  pdb=" N   THR B 144 " --> pdb=" O   ILE B 394 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 169
      removed outlier: 3.836A  pdb=" N   GLU B 164 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   ILE B 288 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE B 240 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ILE B 289 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL B 317 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE B 291 " --> pdb=" O   VAL B 317 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LEU B 342 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   GLY B 318 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS B 344 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 341 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   SER B 371 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE B 343 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 10
      removed outlier: 4.227A  pdb=" N   TYR C   8 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 151
      removed outlier: 5.462A  pdb=" N   ASN C 148 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   ILE C 167 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE C 150 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE C 240 " --> pdb=" O   THR C 290 " (cutoff:3.500A)
      removed outlier: 8.427A  pdb=" N   GLU C 292 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE C 242 " --> pdb=" O   GLU C 292 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ALA C 368 " --> pdb=" O   GLN C 393 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LYS C 395 " --> pdb=" O   ALA C 368 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL C 370 " --> pdb=" O   LYS C 395 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR C 144 " --> pdb=" O   ILE C 394 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 250 through 251

    228 hydrogen bonds defined for protein.
    648 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: 4.41

  Time building geometry restraints manager: 4.02 seconds

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

  Histogram of bond lengths:
        0.90 -     1.08: 1954
        1.08 -     1.27: 5778
        1.27 -     1.46: 1743
        1.46 -     1.65: 3777
        1.65 -     1.83: 42
  Bond restraints: 13294
  Sorted by residual:
  bond pdb=" CG  ASP B 301 "
       pdb=" OD1 ASP B 301 "
    ideal  model  delta    sigma   weight residual
    1.249  1.080  0.169 1.90e-02 2.77e+03 7.93e+01
  bond pdb=" CB  ASP B 301 "
       pdb=" CG  ASP B 301 "
    ideal  model  delta    sigma   weight residual
    1.516  1.322  0.194 2.50e-02 1.60e+03 6.01e+01
  bond pdb=" CE1 TYR C  59 "
       pdb=" HE1 TYR C  59 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   LEU C 351 "
       pdb=" H   LEU C 351 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   LEU B  51 "
       pdb=" H   LEU B  51 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 13289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 18171
        2.30 -     4.60: 4437
        4.60 -     6.91: 987
        6.91 -     9.21: 393
        9.21 -    11.51: 34
  Bond angle restraints: 24022
  Sorted by residual:
  angle pdb=" CA  PHE C 249 "
        pdb=" CB  PHE C 249 "
        pdb=" CG  PHE C 249 "
      ideal   model   delta    sigma   weight residual
     113.80  122.09   -8.29 1.00e+00 1.00e+00 6.87e+01
  angle pdb=" CA  ASN C 236 "
        pdb=" CB  ASN C 236 "
        pdb=" CG  ASN C 236 "
      ideal   model   delta    sigma   weight residual
     112.60  120.58   -7.98 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" C   LEU B  62 "
        pdb=" N   GLY B  63 "
        pdb=" CA  GLY B  63 "
      ideal   model   delta    sigma   weight residual
     120.31  128.40   -8.09 1.02e+00 9.61e-01 6.30e+01
  angle pdb=" CA  ASN C 284 "
        pdb=" CB  ASN C 284 "
        pdb=" CG  ASN C 284 "
      ideal   model   delta    sigma   weight residual
     112.60  120.24   -7.64 1.00e+00 1.00e+00 5.83e+01
  angle pdb=" CA  ASP B 301 "
        pdb=" CB  ASP B 301 "
        pdb=" CG  ASP B 301 "
      ideal   model   delta    sigma   weight residual
     112.60  120.21   -7.61 1.00e+00 1.00e+00 5.79e+01
  ... (remaining 24017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 5349
       16.79 -    33.59: 568
       33.59 -    50.38: 182
       50.38 -    67.17: 97
       67.17 -    83.97: 16
  Dihedral angle restraints: 6212
    sinusoidal: 3390
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" C   ILE B 222 "
           pdb=" N   ILE B 222 "
           pdb=" CA  ILE B 222 "
           pdb=" CB  ILE B 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -140.12   18.12     0      2.50e+00 1.60e-01 5.25e+01
  dihedral pdb=" CA  MET B 239 "
           pdb=" C   MET B 239 "
           pdb=" N   ILE B 240 "
           pdb=" CA  ILE B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  HIS C 372 "
           pdb=" C   HIS C 372 "
           pdb=" N   ARG C 373 "
           pdb=" CA  ARG C 373 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 6209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 703
       0.106 -    0.213: 258
       0.213 -    0.319: 54
       0.319 -    0.425: 7
       0.425 -    0.532: 4
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CA  THR B  64 "
            pdb=" N   THR B  64 "
            pdb=" C   THR B  64 "
            pdb=" CB  THR B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.53 2.00e-01 2.50e+01 7.06e+00
  chirality pdb=" CA  ILE B 222 "
            pdb=" N   ILE B 222 "
            pdb=" C   ILE B 222 "
            pdb=" CB  ILE B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.91    0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" CA  LYS C 434 "
            pdb=" N   LYS C 434 "
            pdb=" C   LYS C 434 "
            pdb=" CB  LYS C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.49e+00
  ... (remaining 1023 not shown)

  Planarity restraints: 2046
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 181 "   -0.316 2.00e-02 2.50e+03   1.10e-01 4.81e+02
        pdb=" CG  TRP C 181 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 181 "    0.072 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 181 "    0.066 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 181 "    0.116 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 181 "    0.043 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 181 "    0.092 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 181 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 181 "    0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 181 "   -0.059 2.00e-02 2.50e+03
        pdb=" HD1 TRP C 181 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE1 TRP C 181 "    0.075 2.00e-02 2.50e+03
        pdb=" HE3 TRP C 181 "    0.126 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C 181 "   -0.107 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C 181 "    0.044 2.00e-02 2.50e+03
        pdb=" HH2 TRP C 181 "   -0.126 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  82 "   -0.267 2.00e-02 2.50e+03   1.09e-01 3.55e+02
        pdb=" CG  TYR B  82 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  82 "    0.074 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  82 "    0.086 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  82 "    0.051 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  82 "    0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  82 "   -0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR B  82 "   -0.201 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  82 "    0.066 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  82 "    0.074 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  82 "    0.031 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  82 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  34 "   -0.679 9.50e-02 1.11e+02   2.47e-01 2.71e+02
        pdb=" NE  ARG B  34 "   -0.084 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  34 "   -0.057 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  34 "   -0.059 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  34 "   -0.026 2.00e-02 2.50e+03
        pdb="HH11 ARG B  34 "    0.208 2.00e-02 2.50e+03
        pdb="HH12 ARG B  34 "   -0.072 2.00e-02 2.50e+03
        pdb="HH21 ARG B  34 "    0.154 2.00e-02 2.50e+03
        pdb="HH22 ARG B  34 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 2043 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 925
        2.18 -     2.79: 23119
        2.79 -     3.39: 37363
        3.39 -     4.00: 47978
        4.00 -     4.60: 71199
  Nonbonded interactions: 180584
  Sorted by model distance:
  nonbonded pdb=" HG  SER C 246 "
            pdb=" O   ASP C 293 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" HG  SER B 247 "
            pdb=" OD1 ASP B 296 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" OD1 ASP C  98 "
            pdb=" HG1 THR C 100 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HH  TYR B 257 "
            pdb=" OD2 ASP B 299 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" HG1 THR C 271 "
            pdb=" OE1 GLU C 274 "
     model   vdw
     1.603 2.450
  ... (remaining 180579 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.230
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     30.070
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2472
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      :  0.016   0.194   6750  Z= 0.975
  Angle     :  2.246  11.081   9128  Z= 1.461
  Chirality :  0.113   0.532   1026
  Planarity :  0.019   0.226   1198
  Dihedral  : 17.124  83.965   2470
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 0.83
  Ramachandran Plot:
    Outliers :  2.65 %
    Allowed  : 12.10 %
    Favored  : 85.25 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  :  9.24 %
    Favored  : 83.87 %
  Cbeta Deviations :  1.28 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.24), residues: 868
  helix: -3.32 (0.20), residues: 303
  sheet: -1.58 (0.76), residues: 45
  loop : -2.27 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.209   0.039   TRP C 181 
 HIS   0.013   0.004   HIS C 155 
 PHE   0.128   0.019   PHE C 249 
 TYR   0.229   0.028   TYR B  82 
 ARG   0.008   0.001   ARG C  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17939 (  228)
  hydrogen bonds       : angle      10.47586 (  648)
  covalent geometry    : bond        0.01568 ( 6750)
  covalent geometry    : angle       2.24587 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 76
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 ASP cc_start: 0.6247 (p0) cc_final: 0.4792 (m-30)
REVERT: B   36 MET cc_start: -0.0763 (OUTLIER) cc_final: -0.2783 (pmt)
REVERT: B   65 GLN cc_start: 0.3000 (tp40) cc_final: 0.1920 (tp40)
REVERT: B  124 ASP cc_start: 0.2300 (OUTLIER) cc_final: 0.2040 (m-30)
REVERT: B  213 GLU cc_start: 0.3711 (OUTLIER) cc_final: 0.2470 (tp30)
REVERT: B  274 GLU cc_start: 0.2338 (OUTLIER) cc_final: 0.1553 (mt-10)
REVERT: B  282 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.0884 (tt)
REVERT: B  284 ASN cc_start: 0.3150 (OUTLIER) cc_final: 0.0099 (m-40)
REVERT: B  301 ASP cc_start: 0.2824 (OUTLIER) cc_final: 0.2159 (t0)
REVERT: B  309 ARG cc_start: 0.4183 (OUTLIER) cc_final: 0.2288 (tpt170)
REVERT: C    1 MET cc_start: 0.2811 (mmt) cc_final: 0.2411 (mmt)
REVERT: C   77 GLU cc_start: 0.0585 (OUTLIER) cc_final: -0.0524 (pp20)
REVERT: C   85 ARG cc_start: 0.3713 (mtm180) cc_final: 0.0640 (ttp80)
REVERT: C  181 TRP cc_start: 0.2747 (OUTLIER) cc_final: 0.2026 (m-10)
REVERT: C  261 LYS cc_start: 0.3104 (tptt) cc_final: 0.2755 (tptp)
REVERT: C  362 LYS cc_start: 0.2445 (OUTLIER) cc_final: 0.0412 (tmmt)
  outliers start: 47
  outliers final: 25
  residues processed: 119
  average time/residue: 0.4227
  time to fit residues: 66.0602
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 61
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  301 ASP
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  309 ARG
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 284 ASN
C  18 ASN
** C  72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.358504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.357093 restraints weight = 26618.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.5392 rms_B_bonded: 0.27
r_work: 0.5373 rms_B_bonded: 0.65 restraints_weight: 0.5000
r_work: 0.5317 rms_B_bonded: 2.23 restraints_weight: 0.2500
r_work (final): 0.5317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2535
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110   6750  Z= 0.235
  Angle     :  0.914  13.356   9128  Z= 0.496
  Chirality :  0.048   0.168   1026
  Planarity :  0.006   0.069   1198
  Dihedral  : 12.783  72.306   1029
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.94 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 13.20 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.83 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.26), residues: 868
  helix: -2.28 (0.26), residues: 292
  sheet: -3.02 (0.43), residues: 114
  loop : -2.11 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 181 
 HIS   0.004   0.002   HIS B   0 
 PHE   0.026   0.003   PHE B 249 
 TYR   0.023   0.002   TYR B 408 
 ARG   0.006   0.001   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05682 (  228)
  hydrogen bonds       : angle       8.26148 (  648)
  covalent geometry    : bond        0.00502 ( 6750)
  covalent geometry    : angle       0.91357 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 62
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1389 (OUTLIER) cc_final: -0.2942 (pmt)
REVERT: B  124 ASP cc_start: 0.1093 (OUTLIER) cc_final: 0.0779 (m-30)
REVERT: B  126 LEU cc_start: 0.0301 (OUTLIER) cc_final: -0.1522 (mt)
REVERT: B  132 THR cc_start: 0.3179 (OUTLIER) cc_final: 0.2575 (p)
REVERT: B  133 TYR cc_start: 0.1971 (OUTLIER) cc_final: 0.1450 (t80)
REVERT: B  263 GLU cc_start: 0.3432 (OUTLIER) cc_final: 0.2822 (tt0)
REVERT: B  274 GLU cc_start: 0.2377 (OUTLIER) cc_final: 0.1502 (mt-10)
REVERT: B  282 LEU cc_start: 0.1746 (OUTLIER) cc_final: 0.1450 (tp)
REVERT: B  284 ASN cc_start: 0.2987 (OUTLIER) cc_final: -0.0557 (m-40)
REVERT: B  309 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.1874 (mmm160)
REVERT: C    1 MET cc_start: 0.2678 (mmt) cc_final: 0.0872 (ttp)
REVERT: C   77 GLU cc_start: 0.0630 (OUTLIER) cc_final: -0.0197 (pp20)
REVERT: C   85 ARG cc_start: 0.3145 (mtm180) cc_final: 0.1449 (ttt180)
REVERT: C  146 MET cc_start: 0.0545 (ptm) cc_final: 0.0286 (ptm)
REVERT: C  181 TRP cc_start: 0.2334 (OUTLIER) cc_final: 0.1709 (m-10)
REVERT: C  261 LYS cc_start: 0.3570 (tptt) cc_final: 0.2843 (tptp)
REVERT: C  276 VAL cc_start: 0.1135 (OUTLIER) cc_final: 0.0246 (t)
REVERT: C  362 LYS cc_start: 0.2215 (OUTLIER) cc_final: -0.0041 (tmmt)
  outliers start: 46
  outliers final: 27
  residues processed: 103
  average time/residue: 0.3872
  time to fit residues: 53.3537
Evaluate side-chains
  95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 54
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue   97 LEU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  424 TYR
Chi-restraints excluded: chain C residue  432 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 85 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
** C  72 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 = 0.5422 r_free = 0.5422 target = 0.362133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5350 r_free = 0.5350 target = 0.351963 restraints weight = 270552.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.5322 rms_B_bonded: 6.78
r_work (final): 0.5322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2417
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   6750  Z= 0.149
  Angle     :  0.705   8.558   9128  Z= 0.382
  Chirality :  0.044   0.150   1026
  Planarity :  0.005   0.073   1198
  Dihedral  : 11.249  77.672   1009
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.45 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 15.25 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.26), residues: 868
  helix: -1.63 (0.28), residues: 308
  sheet: -2.84 (0.45), residues: 112
  loop : -2.15 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 300 
 HIS   0.003   0.001   HIS C   0 
 PHE   0.030   0.002   PHE C 249 
 TYR   0.020   0.001   TYR B 408 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  228)
  hydrogen bonds       : angle       7.29154 (  648)
  covalent geometry    : bond        0.00320 ( 6750)
  covalent geometry    : angle       0.70460 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 54
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1648 (OUTLIER) cc_final: -0.3029 (pmt)
REVERT: B  124 ASP cc_start: 0.0964 (OUTLIER) cc_final: 0.0509 (m-30)
REVERT: B  126 LEU cc_start: -0.0132 (OUTLIER) cc_final: -0.1682 (mt)
REVERT: B  132 THR cc_start: 0.2722 (OUTLIER) cc_final: 0.2101 (p)
REVERT: B  263 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2593 (tt0)
REVERT: B  274 GLU cc_start: 0.2130 (OUTLIER) cc_final: 0.1376 (mt-10)
REVERT: B  284 ASN cc_start: 0.3161 (OUTLIER) cc_final: -0.0363 (p0)
REVERT: B  309 ARG cc_start: 0.4017 (OUTLIER) cc_final: 0.1912 (mmm160)
REVERT: B  360 MET cc_start: 0.1866 (ptt) cc_final: 0.0507 (mmt)
REVERT: C    1 MET cc_start: 0.2296 (mmt) cc_final: 0.0256 (ttp)
REVERT: C   23 VAL cc_start: 0.3928 (OUTLIER) cc_final: 0.3579 (t)
REVERT: C   85 ARG cc_start: 0.3294 (mtm180) cc_final: 0.0064 (ttp80)
REVERT: C   86 ASP cc_start: 0.1102 (OUTLIER) cc_final: 0.0890 (m-30)
REVERT: C  155 HIS cc_start: 0.4005 (OUTLIER) cc_final: 0.2743 (m90)
REVERT: C  181 TRP cc_start: 0.2318 (OUTLIER) cc_final: 0.1678 (m-10)
REVERT: C  297 GLU cc_start: 0.3415 (mt-10) cc_final: 0.3075 (mt-10)
REVERT: C  362 LYS cc_start: 0.1865 (OUTLIER) cc_final: -0.0063 (tmmt)
REVERT: C  372 HIS cc_start: 0.0743 (OUTLIER) cc_final: 0.0258 (p-80)
  outliers start: 36
  outliers final: 16
  residues processed: 87
  average time/residue: 0.4014
  time to fit residues: 47.3374
Evaluate side-chains
  77 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 47
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.6162

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

Flipped N/Q/H residues before XYZ refinement:
C 236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.359433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5333 r_free = 0.5333 target = 0.350365 restraints weight = 271986.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.5310 rms_B_bonded: 6.43
r_work (final): 0.5310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2490
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6750  Z= 0.160
  Angle     :  0.682   7.412   9128  Z= 0.370
  Chirality :  0.043   0.153   1026
  Planarity :  0.005   0.069   1198
  Dihedral  : 10.583  77.182    997
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.91 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 16.28 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.27), residues: 868
  helix: -1.32 (0.30), residues: 300
  sheet: -2.85 (0.46), residues: 114
  loop : -2.04 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 300 
 HIS   0.003   0.001   HIS B   0 
 PHE   0.021   0.002   PHE B 249 
 TYR   0.018   0.002   TYR B 408 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  228)
  hydrogen bonds       : angle       6.92354 (  648)
  covalent geometry    : bond        0.00347 ( 6750)
  covalent geometry    : angle       0.68170 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 51
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1277 (OUTLIER) cc_final: -0.3026 (pmt)
REVERT: B  124 ASP cc_start: 0.0593 (OUTLIER) cc_final: 0.0197 (m-30)
REVERT: B  126 LEU cc_start: -0.0130 (OUTLIER) cc_final: -0.1855 (mt)
REVERT: B  132 THR cc_start: 0.2778 (OUTLIER) cc_final: 0.2216 (p)
REVERT: B  263 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2566 (tt0)
REVERT: B  274 GLU cc_start: 0.2003 (OUTLIER) cc_final: 0.1154 (tp30)
REVERT: B  284 ASN cc_start: 0.2954 (OUTLIER) cc_final: -0.0529 (p0)
REVERT: B  309 ARG cc_start: 0.4327 (OUTLIER) cc_final: 0.2546 (mmm160)
REVERT: B  360 MET cc_start: 0.2332 (ptt) cc_final: 0.0634 (mmt)
REVERT: C    1 MET cc_start: 0.2335 (mmt) cc_final: 0.0164 (ttp)
REVERT: C   23 VAL cc_start: 0.3841 (OUTLIER) cc_final: 0.3621 (t)
REVERT: C   36 MET cc_start: 0.2483 (OUTLIER) cc_final: 0.2022 (tpt)
REVERT: C   85 ARG cc_start: 0.3635 (mtm180) cc_final: 0.0267 (ttp80)
REVERT: C   86 ASP cc_start: 0.1249 (OUTLIER) cc_final: 0.1010 (m-30)
REVERT: C  181 TRP cc_start: 0.2433 (OUTLIER) cc_final: 0.1879 (m-10)
REVERT: C  276 VAL cc_start: 0.0905 (OUTLIER) cc_final: -0.0210 (m)
REVERT: C  362 LYS cc_start: 0.1970 (OUTLIER) cc_final: 0.0220 (tmmt)
  outliers start: 39
  outliers final: 22
  residues processed: 85
  average time/residue: 0.4255
  time to fit residues: 47.6816
Evaluate side-chains
  87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 51
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 6 optimal weight:    0.3980
   chunk 41 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 74 optimal weight:    0.3980
   chunk 55 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   overall best weight:    1.5582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5405 r_free = 0.5405 target = 0.359384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5401 r_free = 0.5401 target = 0.358766 restraints weight = 26929.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.5401 rms_B_bonded: 0.12
r_work: 0.5397 rms_B_bonded: 0.17 restraints_weight: 0.5000
r_work: 0.5384 rms_B_bonded: 0.52 restraints_weight: 0.2500
r_work: 0.5293 rms_B_bonded: 3.92 restraints_weight: 0.1250
r_work (final): 0.5293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2488
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6750  Z= 0.148
  Angle     :  0.634   6.108   9128  Z= 0.344
  Chirality :  0.042   0.152   1026
  Planarity :  0.005   0.072   1198
  Dihedral  : 10.038  81.064    993
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.45 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 16.57 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.27), residues: 868
  helix: -1.10 (0.30), residues: 293
  sheet: -2.52 (0.50), residues: 100
  loop : -2.16 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 300 
 HIS   0.004   0.001   HIS C 372 
 PHE   0.020   0.002   PHE B 249 
 TYR   0.016   0.001   TYR B 408 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03800 (  228)
  hydrogen bonds       : angle       6.74380 (  648)
  covalent geometry    : bond        0.00324 ( 6750)
  covalent geometry    : angle       0.63362 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 53
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1466 (OUTLIER) cc_final: -0.2981 (pmt)
REVERT: B  124 ASP cc_start: 0.0919 (OUTLIER) cc_final: 0.0540 (m-30)
REVERT: B  126 LEU cc_start: 0.0191 (OUTLIER) cc_final: -0.0194 (tp)
REVERT: B  132 THR cc_start: 0.2748 (OUTLIER) cc_final: 0.2173 (p)
REVERT: B  155 HIS cc_start: 0.5877 (OUTLIER) cc_final: 0.3896 (m90)
REVERT: B  263 GLU cc_start: 0.3324 (OUTLIER) cc_final: 0.2801 (tt0)
REVERT: B  274 GLU cc_start: 0.1799 (OUTLIER) cc_final: 0.1172 (mt-10)
REVERT: B  284 ASN cc_start: 0.2967 (OUTLIER) cc_final: -0.0931 (p0)
REVERT: B  309 ARG cc_start: 0.4321 (OUTLIER) cc_final: 0.2795 (mmm160)
REVERT: B  360 MET cc_start: 0.2301 (ptt) cc_final: 0.0716 (mmt)
REVERT: C    1 MET cc_start: 0.1896 (mmt) cc_final: 0.0132 (ttp)
REVERT: C   36 MET cc_start: 0.2295 (OUTLIER) cc_final: 0.1982 (tpt)
REVERT: C   85 ARG cc_start: 0.3771 (mtm180) cc_final: 0.0545 (ttp-170)
REVERT: C  155 HIS cc_start: 0.5082 (OUTLIER) cc_final: 0.3518 (m90)
REVERT: C  181 TRP cc_start: 0.2531 (OUTLIER) cc_final: 0.1931 (m-10)
REVERT: C  261 LYS cc_start: 0.3982 (tptt) cc_final: 0.2303 (tptp)
REVERT: C  274 GLU cc_start: 0.2022 (OUTLIER) cc_final: 0.1240 (mm-30)
REVERT: C  276 VAL cc_start: 0.1306 (OUTLIER) cc_final: 0.0258 (m)
REVERT: C  362 LYS cc_start: 0.2141 (OUTLIER) cc_final: 0.0171 (tmmt)
  outliers start: 42
  outliers final: 23
  residues processed: 89
  average time/residue: 0.4242
  time to fit residues: 50.2836
Evaluate side-chains
  88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 50
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   overall best weight:    2.0082

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.357563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5395 r_free = 0.5395 target = 0.357219 restraints weight = 27009.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.5395 rms_B_bonded: 0.07
r_work: 0.5393 rms_B_bonded: 0.11 restraints_weight: 0.5000
r_work: 0.5387 rms_B_bonded: 0.27 restraints_weight: 0.2500
r_work: 0.5330 rms_B_bonded: 2.33 restraints_weight: 0.1250
r_work (final): 0.5330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2537
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   6750  Z= 0.169
  Angle     :  0.668   6.124   9128  Z= 0.363
  Chirality :  0.043   0.152   1026
  Planarity :  0.006   0.070   1198
  Dihedral  :  9.998  85.218    992
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.52 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 16.13 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.27), residues: 868
  helix: -1.11 (0.30), residues: 292
  sheet: -2.99 (0.44), residues: 115
  loop : -2.14 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 300 
 HIS   0.005   0.001   HIS B   0 
 PHE   0.023   0.002   PHE B 249 
 TYR   0.015   0.002   TYR B 431 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  228)
  hydrogen bonds       : angle       6.81472 (  648)
  covalent geometry    : bond        0.00372 ( 6750)
  covalent geometry    : angle       0.66810 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 51
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1357 (OUTLIER) cc_final: -0.3078 (pmt)
REVERT: B  124 ASP cc_start: 0.1270 (OUTLIER) cc_final: 0.0829 (m-30)
REVERT: B  132 THR cc_start: 0.2835 (OUTLIER) cc_final: 0.2286 (p)
REVERT: B  133 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.1897 (t80)
REVERT: B  155 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.3943 (m90)
REVERT: B  274 GLU cc_start: 0.2127 (OUTLIER) cc_final: 0.1572 (mt-10)
REVERT: B  284 ASN cc_start: 0.3101 (OUTLIER) cc_final: -0.0597 (p0)
REVERT: B  309 ARG cc_start: 0.4495 (OUTLIER) cc_final: 0.2415 (mmm160)
REVERT: C    1 MET cc_start: 0.2197 (mmt) cc_final: 0.0463 (ttp)
REVERT: C  155 HIS cc_start: 0.5180 (OUTLIER) cc_final: 0.3707 (m90)
REVERT: C  181 TRP cc_start: 0.2298 (OUTLIER) cc_final: 0.1764 (m-10)
REVERT: C  274 GLU cc_start: 0.2007 (OUTLIER) cc_final: 0.1351 (mm-30)
REVERT: C  362 LYS cc_start: 0.2408 (OUTLIER) cc_final: 0.0733 (tmmt)
  outliers start: 44
  outliers final: 31
  residues processed: 89
  average time/residue: 0.4273
  time to fit residues: 51.5692
Evaluate side-chains
  92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 49
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  429 SER
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5377 r_free = 0.5377 target = 0.355172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5374 r_free = 0.5374 target = 0.354675 restraints weight = 26786.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.5374 rms_B_bonded: 0.08
r_work: 0.5372 rms_B_bonded: 0.12 restraints_weight: 0.5000
r_work: 0.5366 rms_B_bonded: 0.26 restraints_weight: 0.2500
r_work: 0.5307 rms_B_bonded: 2.26 restraints_weight: 0.1250
r_work (final): 0.5307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2674
moved from start:          0.4981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.139   6750  Z= 0.231
  Angle     :  0.788   7.589   9128  Z= 0.428
  Chirality :  0.046   0.159   1026
  Planarity :  0.007   0.079   1198
  Dihedral  : 10.491  89.274    992
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 13.25 %
    Favored  : 86.52 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 16.13 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.26), residues: 868
  helix: -1.46 (0.29), residues: 286
  sheet: -3.31 (0.43), residues: 110
  loop : -2.31 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 181 
 HIS   0.005   0.002   HIS C 372 
 PHE   0.022   0.002   PHE B 249 
 TYR   0.027   0.002   TYR C 286 
 ARG   0.006   0.001   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  228)
  hydrogen bonds       : angle       7.37600 (  648)
  covalent geometry    : bond        0.00520 ( 6750)
  covalent geometry    : angle       0.78758 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 52
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ARG cc_start: 0.3493 (OUTLIER) cc_final: 0.0632 (tpt170)
REVERT: B   36 MET cc_start: -0.1610 (OUTLIER) cc_final: -0.3346 (pmt)
REVERT: B  124 ASP cc_start: 0.1625 (OUTLIER) cc_final: 0.1289 (m-30)
REVERT: B  132 THR cc_start: 0.2980 (OUTLIER) cc_final: 0.2368 (p)
REVERT: B  133 TYR cc_start: 0.2845 (OUTLIER) cc_final: 0.2359 (t80)
REVERT: B  155 HIS cc_start: 0.5758 (OUTLIER) cc_final: 0.4951 (m90)
REVERT: B  274 GLU cc_start: 0.2200 (OUTLIER) cc_final: 0.1689 (mt-10)
REVERT: B  284 ASN cc_start: 0.3117 (OUTLIER) cc_final: -0.0928 (p0)
REVERT: B  309 ARG cc_start: 0.5135 (OUTLIER) cc_final: 0.1185 (mpt180)
REVERT: C    1 MET cc_start: 0.2584 (mmt) cc_final: 0.2136 (mmt)
REVERT: C   85 ARG cc_start: 0.3986 (mtm180) cc_final: 0.0628 (ttp80)
REVERT: C  155 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.4017 (m90)
REVERT: C  181 TRP cc_start: 0.2430 (OUTLIER) cc_final: 0.1851 (m-10)
REVERT: C  274 GLU cc_start: 0.1640 (OUTLIER) cc_final: 0.1183 (mm-30)
REVERT: C  276 VAL cc_start: 0.1165 (OUTLIER) cc_final: -0.0045 (m)
REVERT: C  362 LYS cc_start: 0.2780 (OUTLIER) cc_final: 0.0973 (tmmt)
  outliers start: 52
  outliers final: 33
  residues processed: 97
  average time/residue: 0.4286
  time to fit residues: 54.5688
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 50
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C 148 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 = 0.5385 r_free = 0.5385 target = 0.356757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5319 r_free = 0.5319 target = 0.348269 restraints weight = 272839.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.5292 rms_B_bonded: 6.15
r_work (final): 0.5292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2667
moved from start:          0.5314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   6750  Z= 0.201
  Angle     :  0.718   6.681   9128  Z= 0.391
  Chirality :  0.044   0.160   1026
  Planarity :  0.006   0.069   1198
  Dihedral  : 10.292  90.342    991
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.33 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 17.45 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.26), residues: 868
  helix: -1.55 (0.28), residues: 304
  sheet: -3.29 (0.43), residues: 113
  loop : -2.44 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 300 
 HIS   0.007   0.001   HIS B   0 
 PHE   0.025   0.002   PHE B 242 
 TYR   0.020   0.002   TYR C 286 
 ARG   0.006   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04137 (  228)
  hydrogen bonds       : angle       7.25363 (  648)
  covalent geometry    : bond        0.00445 ( 6750)
  covalent geometry    : angle       0.71768 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 48
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 TYR cc_start: 0.4237 (OUTLIER) cc_final: 0.1978 (t80)
REVERT: B   10 ARG cc_start: 0.3266 (OUTLIER) cc_final: -0.0206 (tpt170)
REVERT: B   36 MET cc_start: -0.1760 (OUTLIER) cc_final: -0.3443 (pmt)
REVERT: B   58 ARG cc_start: 0.3117 (OUTLIER) cc_final: -0.1683 (mmt90)
REVERT: B  124 ASP cc_start: 0.0584 (OUTLIER) cc_final: 0.0230 (m-30)
REVERT: B  132 THR cc_start: 0.2801 (OUTLIER) cc_final: 0.2229 (p)
REVERT: B  133 TYR cc_start: 0.2650 (OUTLIER) cc_final: 0.2133 (t80)
REVERT: B  155 HIS cc_start: 0.5561 (OUTLIER) cc_final: 0.4703 (m90)
REVERT: B  263 GLU cc_start: 0.2718 (OUTLIER) cc_final: 0.2076 (tt0)
REVERT: B  284 ASN cc_start: 0.2804 (OUTLIER) cc_final: -0.1046 (p0)
REVERT: B  309 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.3444 (mmm-85)
REVERT: C    1 MET cc_start: 0.2867 (mmt) cc_final: 0.2402 (mmt)
REVERT: C   82 TYR cc_start: 0.2040 (m-80) cc_final: 0.1117 (m-80)
REVERT: C   85 ARG cc_start: 0.4065 (mtm180) cc_final: 0.0632 (ttp-170)
REVERT: C  155 HIS cc_start: 0.5175 (OUTLIER) cc_final: 0.3792 (m90)
REVERT: C  181 TRP cc_start: 0.2393 (OUTLIER) cc_final: 0.1856 (m-10)
REVERT: C  261 LYS cc_start: 0.3934 (tptt) cc_final: 0.2327 (tptp)
REVERT: C  274 GLU cc_start: 0.1444 (OUTLIER) cc_final: 0.1204 (mm-30)
REVERT: C  362 LYS cc_start: 0.2747 (OUTLIER) cc_final: 0.0882 (tmmt)
  outliers start: 46
  outliers final: 31
  residues processed: 90
  average time/residue: 0.4416
  time to fit residues: 52.2209
Evaluate side-chains
  93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 47
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 TYR
Chi-restraints excluded: chain B residue   10 ARG
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  220 GLU
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  278 TYR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 41 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0770
   chunk 79 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
C 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5411 r_free = 0.5411 target = 0.360235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.351667 restraints weight = 271714.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.5321 rms_B_bonded: 6.22
r_work (final): 0.5321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2473
moved from start:          0.5566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6750  Z= 0.120
  Angle     :  0.584   5.487   9128  Z= 0.315
  Chirality :  0.041   0.144   1026
  Planarity :  0.004   0.069   1198
  Dihedral  :  9.364  90.488    988
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.95 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 19.50 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.27), residues: 868
  helix: -1.04 (0.30), residues: 302
  sheet: -2.79 (0.48), residues: 101
  loop : -2.44 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 300 
 HIS   0.002   0.001   HIS B   0 
 PHE   0.020   0.002   PHE B 242 
 TYR   0.014   0.001   TYR B 408 
 ARG   0.003   0.001   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 (  228)
  hydrogen bonds       : angle       6.51127 (  648)
  covalent geometry    : bond        0.00258 ( 6750)
  covalent geometry    : angle       0.58425 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 50
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1679 (OUTLIER) cc_final: -0.3330 (pmt)
REVERT: B  132 THR cc_start: 0.2401 (OUTLIER) cc_final: 0.1791 (p)
REVERT: B  155 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.3472 (m90)
REVERT: B  263 GLU cc_start: 0.2756 (OUTLIER) cc_final: 0.2197 (tt0)
REVERT: B  284 ASN cc_start: 0.2337 (OUTLIER) cc_final: -0.1534 (p0)
REVERT: B  309 ARG cc_start: 0.4285 (OUTLIER) cc_final: 0.3866 (mmm-85)
REVERT: C    1 MET cc_start: 0.2664 (mmt) cc_final: 0.2195 (mmt)
REVERT: C   36 MET cc_start: 0.1965 (OUTLIER) cc_final: 0.1445 (tpt)
REVERT: C   82 TYR cc_start: 0.1801 (m-80) cc_final: 0.0983 (m-80)
REVERT: C   85 ARG cc_start: 0.3922 (mtm180) cc_final: 0.0542 (ttp-170)
REVERT: C  155 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.3398 (m90)
REVERT: C  181 TRP cc_start: 0.2165 (OUTLIER) cc_final: 0.1601 (m-10)
REVERT: C  261 LYS cc_start: 0.4239 (tptt) cc_final: 0.2412 (tptp)
REVERT: C  362 LYS cc_start: 0.2291 (OUTLIER) cc_final: 0.0691 (tmmt)
  outliers start: 31
  outliers final: 18
  residues processed: 78
  average time/residue: 0.4301
  time to fit residues: 44.4533
Evaluate side-chains
  77 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 49
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  389 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 14 optimal weight:    0.1980
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.0388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.358200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.5330 r_free = 0.5330 target = 0.349480 restraints weight = 269086.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.5305 rms_B_bonded: 6.22
r_work (final): 0.5305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2601
moved from start:          0.5626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6750  Z= 0.166
  Angle     :  0.655   6.279   9128  Z= 0.354
  Chirality :  0.043   0.158   1026
  Planarity :  0.006   0.071   1198
  Dihedral  :  9.577  90.199    986
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.52 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.65 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.26), residues: 868
  helix: -1.23 (0.29), residues: 298
  sheet: -3.03 (0.47), residues: 101
  loop : -2.41 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 303 
 HIS   0.004   0.001   HIS B   0 
 PHE   0.019   0.002   PHE B 249 
 TYR   0.018   0.002   TYR C 286 
 ARG   0.005   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  228)
  hydrogen bonds       : angle       6.73374 (  648)
  covalent geometry    : bond        0.00365 ( 6750)
  covalent geometry    : angle       0.65461 ( 9128)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 50
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: -0.1524 (OUTLIER) cc_final: -0.3109 (pmt)
REVERT: B  132 THR cc_start: 0.2725 (OUTLIER) cc_final: 0.2225 (p)
REVERT: B  155 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.3563 (m90)
REVERT: B  263 GLU cc_start: 0.2638 (OUTLIER) cc_final: 0.2020 (tt0)
REVERT: B  284 ASN cc_start: 0.2542 (OUTLIER) cc_final: -0.1541 (p0)
REVERT: B  309 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.4318 (mmm-85)
REVERT: C    1 MET cc_start: 0.2701 (mmt) cc_final: 0.2342 (mmt)
REVERT: C   36 MET cc_start: 0.2288 (OUTLIER) cc_final: 0.1755 (tpt)
REVERT: C   82 TYR cc_start: 0.2207 (m-80) cc_final: 0.1266 (m-80)
REVERT: C   85 ARG cc_start: 0.3905 (mtm180) cc_final: 0.0518 (ttp-170)
REVERT: C  155 HIS cc_start: 0.5315 (OUTLIER) cc_final: 0.4010 (m90)
REVERT: C  181 TRP cc_start: 0.2125 (OUTLIER) cc_final: 0.1609 (m-10)
REVERT: C  261 LYS cc_start: 0.4312 (tptt) cc_final: 0.2536 (tptp)
REVERT: C  362 LYS cc_start: 0.2688 (OUTLIER) cc_final: 0.1093 (tmmt)
  outliers start: 30
  outliers final: 18
  residues processed: 77
  average time/residue: 0.4578
  time to fit residues: 46.9593
Evaluate side-chains
  78 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 50
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   58 ARG
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  155 HIS
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  263 GLU
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  430 PHE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain C residue   36 MET
Chi-restraints excluded: chain C residue   66 LYS
Chi-restraints excluded: chain C residue   72 ASN
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  155 HIS
Chi-restraints excluded: chain C residue  181 TRP
Chi-restraints excluded: chain C residue  278 TYR
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  362 LYS
Chi-restraints excluded: chain C residue  367 THR
Chi-restraints excluded: chain C residue  390 ASN
Chi-restraints excluded: chain C residue  424 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 69 optimal weight:    0.3980
   chunk 41 optimal weight:    0.0010
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 71 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5407 r_free = 0.5407 target = 0.358848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5400 r_free = 0.5400 target = 0.357619 restraints weight = 27094.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.5400 rms_B_bonded: 0.24
r_work: 0.5391 rms_B_bonded: 0.39 restraints_weight: 0.5000
r_work: 0.5353 rms_B_bonded: 1.48 restraints_weight: 0.2500
r_work (final): 0.5353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2447
moved from start:          0.5824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6750  Z= 0.113
  Angle     :  0.564   5.114   9128  Z= 0.303
  Chirality :  0.041   0.143   1026
  Planarity :  0.004   0.067   1198
  Dihedral  :  9.058  91.046    986
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.06 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 19.50 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.27), residues: 868
  helix: -0.93 (0.30), residues: 303
  sheet: -2.72 (0.49), residues: 101
  loop : -2.40 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 300 
 HIS   0.002   0.001   HIS B   0 
 PHE   0.018   0.001   PHE B 242 
 TYR   0.014   0.001   TYR B 408 
 ARG   0.004   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  228)
  hydrogen bonds       : angle       6.28579 (  648)
  covalent geometry    : bond        0.00248 ( 6750)
  covalent geometry    : angle       0.56377 ( 9128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4934.16 seconds
wall clock time: 85 minutes 33.71 seconds (5133.71 seconds total)