Starting phenix.real_space_refine
on Fri Aug 22 20:13:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x9p_38178/08_2025/8x9p_38178.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    4835      2.51       5
     N    1307      2.21       5
     O    1474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7669
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3423
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418}
    Chain: "B"
      Number of atoms: 3359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3359
          Classifications: {'peptide': 427}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406}
    Chain: "C"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 887
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 2, 'TRANS': 104}
  Time building chain proxies: 1.80, per 1000 atoms: 0.23
  Number of scatterers: 7669
  At special positions: 0
  Unit cell: (106.24, 79.68, 99.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1474      8.00
     N    1307      7.00
     C    4835      6.00
    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: 0.52
  Conformation dependent library (CDL) restraints added in 290.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      57.5% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.261A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 3.606A  pdb=" N   PHE A  87 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.638A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 162
      removed outlier: 4.333A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.504A  pdb=" N   SER A 178 " --> pdb=" O   PRO A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.541A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.896A  pdb=" N   PHE A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
    Processing helix  chain 'A' and resid 287 through 297
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 339
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.726A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   HIS A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   MET A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 4.380A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 438
      removed outlier: 3.975A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.506A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 78
      removed outlier: 3.511A  pdb=" N   SER B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 109 through 127
      removed outlier: 4.925A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 4.331A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 4.592A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
      removed outlier: 3.853A  pdb=" N   MET B 299 " --> pdb=" O   ALA B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.706A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 374 through 391
      removed outlier: 3.782A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
      removed outlier: 3.587A  pdb=" N   GLY B 400 " --> pdb=" O   HIS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 4.089A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 256
    Processing helix  chain 'C' and resid 261 through 281
    Processing helix  chain 'C' and resid 281 through 296
    Processing helix  chain 'C' and resid 303 through 334
      removed outlier: 3.574A  pdb=" N   LEU C 307 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN C 317 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.804A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A   5 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 7.148A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   CYS A 376 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92
      removed outlier: 8.386A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR B 166 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ASP B 203 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 11.860A  pdb=" N   PHE B 270 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53

    421 hydrogen bonds defined for protein.
    1218 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: 0.81

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2499
        1.34 -     1.46: 1288
        1.46 -     1.58: 3969
        1.58 -     1.70: 0
        1.70 -     1.82: 83
  Bond restraints: 7839
  Sorted by residual:
  bond pdb=" CB  ILE B  16 "
       pdb=" CG2 ILE B  16 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.65e+00
  bond pdb=" CG1 ILE B  16 "
       pdb=" CD1 ILE B  16 "
    ideal  model  delta    sigma   weight residual
    1.513  1.450  0.063 3.90e-02 6.57e+02 2.62e+00
  bond pdb=" CB  MET B 233 "
       pdb=" CG  MET B 233 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.34e+00
  bond pdb=" C   CYS A   4 "
       pdb=" N   ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.335  1.314  0.021 1.41e-02 5.03e+03 2.27e+00
  bond pdb=" CG1 ILE A 188 "
       pdb=" CD1 ILE A 188 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.86e+00
  ... (remaining 7834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 10460
        2.32 -     4.64: 130
        4.64 -     6.96: 21
        6.96 -     9.28: 6
        9.28 -    11.61: 2
  Bond angle restraints: 10619
  Sorted by residual:
  angle pdb=" N   VAL B 180 "
        pdb=" CA  VAL B 180 "
        pdb=" C   VAL B 180 "
      ideal   model   delta    sigma   weight residual
     113.20  109.77    3.43 9.60e-01 1.09e+00 1.28e+01
  angle pdb=" CA  TRP C 311 "
        pdb=" CB  TRP C 311 "
        pdb=" CG  TRP C 311 "
      ideal   model   delta    sigma   weight residual
     113.60  107.01    6.59 1.90e+00 2.77e-01 1.20e+01
  angle pdb=" CA  LEU B 151 "
        pdb=" CB  LEU B 151 "
        pdb=" CG  LEU B 151 "
      ideal   model   delta    sigma   weight residual
     116.30  127.91  -11.61 3.50e+00 8.16e-02 1.10e+01
  angle pdb=" CA  GLN C 285 "
        pdb=" CB  GLN C 285 "
        pdb=" CG  GLN C 285 "
      ideal   model   delta    sigma   weight residual
     114.10  120.67   -6.57 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" CB  MET B 233 "
        pdb=" CG  MET B 233 "
        pdb=" SD  MET B 233 "
      ideal   model   delta    sigma   weight residual
     112.70  102.95    9.75 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 10614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4070
       17.99 -    35.99: 487
       35.99 -    53.98: 92
       53.98 -    71.98: 23
       71.98 -    89.97: 6
  Dihedral angle restraints: 4678
    sinusoidal: 1874
      harmonic: 2804
  Sorted by residual:
  dihedral pdb=" CA  MET B   1 "
           pdb=" C   MET B   1 "
           pdb=" N   ARG B   2 "
           pdb=" CA  ARG B   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLN B 384 "
           pdb=" C   GLN B 384 "
           pdb=" N   PHE B 385 "
           pdb=" CA  PHE B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.24  -17.76     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  ASN B 195 "
           pdb=" CB  ASN B 195 "
           pdb=" CG  ASN B 195 "
           pdb=" OD1 ASN B 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.81   73.81     2      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 4675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 832
       0.045 -    0.089: 255
       0.089 -    0.134: 65
       0.134 -    0.178: 5
       0.178 -    0.223: 1
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CB  ILE B  16 "
            pdb=" CA  ILE B  16 "
            pdb=" CG1 ILE B  16 "
            pdb=" CG2 ILE B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 363 "
            pdb=" CA  VAL A 363 "
            pdb=" CG1 VAL A 363 "
            pdb=" CG2 VAL A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CA  MET C 313 "
            pdb=" N   MET C 313 "
            pdb=" C   MET C 313 "
            pdb=" CB  MET C 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 286 "   -0.025 2.00e-02 2.50e+03   1.85e-02 6.00e+00
        pdb=" CG  PHE C 286 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 286 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 286 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 286 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 286 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 316 "   -0.018 2.00e-02 2.50e+03   1.83e-02 5.83e+00
        pdb=" CG  PHE C 316 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 316 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 316 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 316 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 316 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 316 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 385 "    0.015 2.00e-02 2.50e+03   1.46e-02 3.71e+00
        pdb=" CG  PHE B 385 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 385 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 385 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 385 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 385 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 385 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1393 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 225
        2.70 -     3.25: 8246
        3.25 -     3.80: 13014
        3.80 -     4.35: 16607
        4.35 -     4.90: 27070
  Nonbonded interactions: 65162
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 285 "
            pdb=" OE1 GLU B 288 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" N   GLU B 407 "
            pdb=" OE1 GLU B 407 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OG  SER B 145 "
            pdb=" OG  SER B 188 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY B  10 "
            pdb=" ND2 ASN B  14 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" NE2 GLN A 301 "
            pdb=" O   CYS A 305 "
     model   vdw
     2.257 3.120
  ... (remaining 65157 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
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      :  0.004   0.063   7839  Z= 0.171
  Angle     :  0.671  11.605  10619  Z= 0.352
  Chirality :  0.044   0.223   1158
  Planarity :  0.004   0.037   1396
  Dihedral  : 16.057  89.973   2880
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 21.44 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.27), residues: 967
  helix:  0.63 (0.23), residues: 479
  sheet:  0.80 (0.47), residues: 135
  loop : -0.06 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 391 
 TYR   0.011   0.001   TYR A 399 
 PHE   0.042   0.002   PHE C 316 
 TRP   0.025   0.002   TRP C 311 
 HIS   0.004   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7839)
  covalent geometry    : angle       0.67071 (10619)
  hydrogen bonds       : bond        0.14521 (  421)
  hydrogen bonds       : angle       6.52759 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6177 (tmm) cc_final: 0.5879 (tmm)
REVERT: A  199 ASP cc_start: 0.7970 (t0) cc_final: 0.7658 (t0)
REVERT: A  217 LEU cc_start: 0.8496 (mt) cc_final: 0.7738 (mt)
REVERT: A  272 TYR cc_start: 0.8026 (t80) cc_final: 0.7676 (t80)
REVERT: A  313 MET cc_start: 0.7696 (mmm) cc_final: 0.7325 (tmm)
REVERT: B   65 LEU cc_start: 0.8115 (mm) cc_final: 0.7566 (mm)
REVERT: B  207 LEU cc_start: 0.7547 (mt) cc_final: 0.7154 (mt)
REVERT: B  226 ASN cc_start: 0.8065 (m-40) cc_final: 0.7558 (m110)
REVERT: B  257 MET cc_start: 0.7956 (tpp) cc_final: 0.7233 (mmt)
REVERT: B  364 SER cc_start: 0.8579 (p) cc_final: 0.8342 (m)
REVERT: B  406 MET cc_start: 0.9029 (mmm) cc_final: 0.8805 (mmt)
REVERT: C  231 VAL cc_start: 0.7931 (p) cc_final: 0.7357 (m)
REVERT: C  244 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8295 (pttt)
REVERT: C  267 LEU cc_start: 0.8871 (mm) cc_final: 0.8431 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0630
  time to fit residues: 17.2509
Evaluate side-chains
  135 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 195 ASN
B 291 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.136695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102444 restraints weight = 16133.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.106651 restraints weight = 8689.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.109139 restraints weight = 6242.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.110629 restraints weight = 5201.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.111526 restraints weight = 4685.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   7839  Z= 0.256
  Angle     :  0.706  12.365  10619  Z= 0.374
  Chirality :  0.047   0.179   1158
  Planarity :  0.005   0.060   1396
  Dihedral  :  4.337  16.273   1055
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.72 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.27), residues: 967
  helix:  0.44 (0.23), residues: 479
  sheet:  0.14 (0.43), residues: 148
  loop : -0.18 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 282 
 TYR   0.018   0.002   TYR A 408 
 PHE   0.035   0.003   PHE C 316 
 TRP   0.014   0.002   TRP B  21 
 HIS   0.009   0.002   HIS C 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 7839)
  covalent geometry    : angle       0.70648 (10619)
  hydrogen bonds       : bond        0.04512 (  421)
  hydrogen bonds       : angle       5.14530 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8170 (t0) cc_final: 0.7859 (t0)
REVERT: A  213 CYS cc_start: 0.8758 (t) cc_final: 0.8467 (t)
REVERT: A  272 TYR cc_start: 0.8136 (t80) cc_final: 0.7810 (t80)
REVERT: B  207 LEU cc_start: 0.8033 (mt) cc_final: 0.7524 (mt)
REVERT: B  213 ARG cc_start: 0.7954 (ppt170) cc_final: 0.7686 (ttp80)
REVERT: B  227 HIS cc_start: 0.7674 (t-90) cc_final: 0.7379 (t-170)
REVERT: B  364 SER cc_start: 0.8691 (p) cc_final: 0.8377 (m)
REVERT: C  241 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: C  244 LYS cc_start: 0.8745 (ptmt) cc_final: 0.8461 (pttm)
REVERT: C  246 THR cc_start: 0.8612 (p) cc_final: 0.8253 (p)
REVERT: C  250 PHE cc_start: 0.8402 (m-80) cc_final: 0.8175 (m-80)
REVERT: C  267 LEU cc_start: 0.8927 (mm) cc_final: 0.8487 (mm)
  outliers start: 27
  outliers final: 21
  residues processed: 171
  average time/residue: 0.0564
  time to fit residues: 13.6321
Evaluate side-chains
  154 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.138988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.104260 restraints weight = 15806.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.108675 restraints weight = 8428.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.111307 restraints weight = 5995.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.112864 restraints weight = 4968.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.113828 restraints weight = 4463.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7839  Z= 0.135
  Angle     :  0.615  12.734  10619  Z= 0.314
  Chirality :  0.043   0.133   1158
  Planarity :  0.005   0.096   1396
  Dihedral  :  4.160  16.082   1055
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.12 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.27), residues: 967
  helix:  0.59 (0.23), residues: 490
  sheet:  0.70 (0.45), residues: 127
  loop : -0.23 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 282 
 TYR   0.043   0.001   TYR A  24 
 PHE   0.027   0.002   PHE B 408 
 TRP   0.037   0.002   TRP C 311 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7839)
  covalent geometry    : angle       0.61472 (10619)
  hydrogen bonds       : bond        0.03916 (  421)
  hydrogen bonds       : angle       4.89277 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ASN cc_start: 0.7923 (p0) cc_final: 0.7584 (p0)
REVERT: A  199 ASP cc_start: 0.8118 (t0) cc_final: 0.7821 (t0)
REVERT: A  213 CYS cc_start: 0.8813 (t) cc_final: 0.8458 (t)
REVERT: A  228 ASN cc_start: 0.8039 (m110) cc_final: 0.7808 (m-40)
REVERT: A  272 TYR cc_start: 0.8088 (t80) cc_final: 0.7852 (t80)
REVERT: B   73 MET cc_start: 0.4951 (mpt) cc_final: 0.4446 (mpp)
REVERT: B  207 LEU cc_start: 0.7789 (mt) cc_final: 0.7247 (mt)
REVERT: B  226 ASN cc_start: 0.8185 (m-40) cc_final: 0.7774 (m110)
REVERT: B  227 HIS cc_start: 0.7655 (t-90) cc_final: 0.7382 (t-170)
REVERT: B  364 SER cc_start: 0.8704 (p) cc_final: 0.8397 (m)
REVERT: B  406 MET cc_start: 0.8995 (mmm) cc_final: 0.8686 (mmm)
REVERT: C  244 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8324 (ptpt)
REVERT: C  252 TRP cc_start: 0.7933 (m100) cc_final: 0.7296 (m100)
REVERT: C  260 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5830 (tp)
REVERT: C  267 LEU cc_start: 0.8909 (mm) cc_final: 0.8491 (mm)
REVERT: C  281 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6748 (tt0)
REVERT: C  284 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8312 (ptmt)
REVERT: C  311 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8350 (t60)
  outliers start: 32
  outliers final: 19
  residues processed: 177
  average time/residue: 0.0639
  time to fit residues: 15.7116
Evaluate side-chains
  149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  266 ASP
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  313 MET
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0170
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 HIS
B  37 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.139419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.105089 restraints weight = 16076.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.109417 restraints weight = 8593.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.112106 restraints weight = 6108.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.113692 restraints weight = 5044.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.114328 restraints weight = 4518.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7839  Z= 0.121
  Angle     :  0.614  11.884  10619  Z= 0.308
  Chirality :  0.042   0.148   1158
  Planarity :  0.004   0.073   1396
  Dihedral  :  4.099  20.601   1055
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.24 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.27), residues: 967
  helix:  0.59 (0.23), residues: 489
  sheet:  0.51 (0.45), residues: 131
  loop : -0.23 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 339 
 TYR   0.029   0.001   TYR A  24 
 PHE   0.022   0.001   PHE B 408 
 TRP   0.032   0.002   TRP C 311 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7839)
  covalent geometry    : angle       0.61437 (10619)
  hydrogen bonds       : bond        0.03692 (  421)
  hydrogen bonds       : angle       4.77346 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8100 (t0) cc_final: 0.7806 (t0)
REVERT: A  213 CYS cc_start: 0.8765 (t) cc_final: 0.8394 (t)
REVERT: A  228 ASN cc_start: 0.8042 (m110) cc_final: 0.7790 (m-40)
REVERT: A  341 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6646 (mm)
REVERT: B   73 MET cc_start: 0.4959 (mpt) cc_final: 0.4623 (mpp)
REVERT: B  226 ASN cc_start: 0.8164 (m-40) cc_final: 0.7719 (m110)
REVERT: B  227 HIS cc_start: 0.7597 (t-90) cc_final: 0.7222 (t-170)
REVERT: B  363 MET cc_start: 0.8101 (tpp) cc_final: 0.7718 (tpp)
REVERT: B  364 SER cc_start: 0.8670 (p) cc_final: 0.8335 (m)
REVERT: B  406 MET cc_start: 0.9042 (mmm) cc_final: 0.8666 (mmm)
REVERT: C  250 PHE cc_start: 0.8457 (m-10) cc_final: 0.8213 (m-10)
REVERT: C  281 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6643 (tt0)
  outliers start: 34
  outliers final: 21
  residues processed: 163
  average time/residue: 0.0537
  time to fit residues: 12.4835
Evaluate side-chains
  147 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 245 GLN
B 347 ASN
C 327 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.137903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.106150 restraints weight = 16091.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.107928 restraints weight = 8615.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.109250 restraints weight = 6960.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.109917 restraints weight = 6464.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.110179 restraints weight = 5996.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7839  Z= 0.145
  Angle     :  0.615  10.930  10619  Z= 0.311
  Chirality :  0.042   0.131   1158
  Planarity :  0.004   0.070   1396
  Dihedral  :  4.003  16.443   1055
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.88 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.27), residues: 967
  helix:  0.69 (0.23), residues: 483
  sheet:  0.40 (0.45), residues: 132
  loop : -0.20 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 339 
 TYR   0.021   0.001   TYR A  24 
 PHE   0.018   0.002   PHE B 389 
 TRP   0.027   0.002   TRP C 311 
 HIS   0.005   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7839)
  covalent geometry    : angle       0.61546 (10619)
  hydrogen bonds       : bond        0.03688 (  421)
  hydrogen bonds       : angle       4.66857 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.8709 (mmm) cc_final: 0.8357 (mmt)
REVERT: A  199 ASP cc_start: 0.8071 (t0) cc_final: 0.7777 (t0)
REVERT: A  213 CYS cc_start: 0.8865 (t) cc_final: 0.8510 (t)
REVERT: A  217 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8187 (mt)
REVERT: A  228 ASN cc_start: 0.8182 (m110) cc_final: 0.7890 (m110)
REVERT: B    1 MET cc_start: 0.7697 (mmt) cc_final: 0.7396 (pmm)
REVERT: B   73 MET cc_start: 0.5203 (mpt) cc_final: 0.4859 (mpp)
REVERT: B  205 GLU cc_start: 0.6943 (mp0) cc_final: 0.6712 (mp0)
REVERT: B  207 LEU cc_start: 0.7886 (mt) cc_final: 0.7288 (mt)
REVERT: B  226 ASN cc_start: 0.8166 (m-40) cc_final: 0.7843 (m110)
REVERT: B  227 HIS cc_start: 0.7663 (t-90) cc_final: 0.7363 (t-170)
REVERT: B  364 SER cc_start: 0.8774 (p) cc_final: 0.8439 (m)
REVERT: B  406 MET cc_start: 0.9216 (mmm) cc_final: 0.8850 (mmm)
REVERT: C  250 PHE cc_start: 0.8455 (m-10) cc_final: 0.8232 (m-10)
REVERT: C  263 ASP cc_start: 0.8424 (m-30) cc_final: 0.7952 (m-30)
REVERT: C  290 VAL cc_start: 0.8900 (t) cc_final: 0.8638 (p)
  outliers start: 34
  outliers final: 29
  residues processed: 170
  average time/residue: 0.0601
  time to fit residues: 14.5427
Evaluate side-chains
  157 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 92 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 ASN
B  37 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.137154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102877 restraints weight = 16143.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.106879 restraints weight = 9011.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.109325 restraints weight = 6574.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.110774 restraints weight = 5508.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.111590 restraints weight = 4981.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7839  Z= 0.152
  Angle     :  0.625  12.245  10619  Z= 0.318
  Chirality :  0.042   0.135   1158
  Planarity :  0.004   0.085   1396
  Dihedral  :  4.023  16.083   1055
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.12 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.27), residues: 967
  helix:  0.68 (0.23), residues: 483
  sheet:  0.28 (0.45), residues: 132
  loop : -0.21 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 282 
 TYR   0.040   0.001   TYR A  24 
 PHE   0.018   0.002   PHE B 270 
 TRP   0.025   0.002   TRP C 311 
 HIS   0.005   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7839)
  covalent geometry    : angle       0.62511 (10619)
  hydrogen bonds       : bond        0.03767 (  421)
  hydrogen bonds       : angle       4.73798 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.8710 (mmm) cc_final: 0.8389 (mmt)
REVERT: A  199 ASP cc_start: 0.8067 (t0) cc_final: 0.7791 (t0)
REVERT: A  213 CYS cc_start: 0.8708 (t) cc_final: 0.8385 (t)
REVERT: A  228 ASN cc_start: 0.8176 (m110) cc_final: 0.7883 (m110)
REVERT: A  313 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6493 (tmm)
REVERT: B    1 MET cc_start: 0.7631 (mmt) cc_final: 0.7130 (pmm)
REVERT: B   73 MET cc_start: 0.5137 (mpt) cc_final: 0.4816 (mpp)
REVERT: B  205 GLU cc_start: 0.6905 (mp0) cc_final: 0.6578 (mp0)
REVERT: B  207 LEU cc_start: 0.7887 (mt) cc_final: 0.7310 (mt)
REVERT: B  226 ASN cc_start: 0.8193 (m-40) cc_final: 0.7706 (m110)
REVERT: B  227 HIS cc_start: 0.7704 (t-90) cc_final: 0.7433 (t-170)
REVERT: B  364 SER cc_start: 0.8749 (p) cc_final: 0.8425 (m)
REVERT: B  383 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7341 (mp0)
REVERT: B  406 MET cc_start: 0.9054 (mmm) cc_final: 0.8707 (mmm)
REVERT: C  244 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8360 (ptpt)
REVERT: C  250 PHE cc_start: 0.8557 (m-10) cc_final: 0.8307 (m-10)
  outliers start: 36
  outliers final: 26
  residues processed: 161
  average time/residue: 0.0526
  time to fit residues: 12.6740
Evaluate side-chains
  153 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 19 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 266 HIS
B  37 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.136494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.104857 restraints weight = 16140.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.107933 restraints weight = 10079.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.108556 restraints weight = 7287.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.109342 restraints weight = 6832.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.110556 restraints weight = 6608.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7839  Z= 0.155
  Angle     :  0.628  11.201  10619  Z= 0.322
  Chirality :  0.042   0.156   1158
  Planarity :  0.004   0.078   1396
  Dihedral  :  4.048  15.969   1055
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.60 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.27), residues: 967
  helix:  0.69 (0.23), residues: 482
  sheet:  0.36 (0.46), residues: 128
  loop : -0.27 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 282 
 TYR   0.042   0.002   TYR A  24 
 PHE   0.016   0.002   PHE B 408 
 TRP   0.033   0.002   TRP C 311 
 HIS   0.008   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7839)
  covalent geometry    : angle       0.62807 (10619)
  hydrogen bonds       : bond        0.03708 (  421)
  hydrogen bonds       : angle       4.75225 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8394 (m-30) cc_final: 0.8114 (m-30)
REVERT: A  105 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7712 (ttm-80)
REVERT: A  154 MET cc_start: 0.8733 (mmm) cc_final: 0.8426 (mmt)
REVERT: A  199 ASP cc_start: 0.8067 (t0) cc_final: 0.7807 (t0)
REVERT: A  213 CYS cc_start: 0.8724 (t) cc_final: 0.8429 (t)
REVERT: A  228 ASN cc_start: 0.8241 (m110) cc_final: 0.7937 (m110)
REVERT: A  313 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6392 (tmm)
REVERT: B    1 MET cc_start: 0.7534 (mmt) cc_final: 0.7060 (pmm)
REVERT: B   19 LYS cc_start: 0.9055 (tptm) cc_final: 0.8744 (tppt)
REVERT: B   73 MET cc_start: 0.5108 (mpt) cc_final: 0.4646 (mpp)
REVERT: B  205 GLU cc_start: 0.6861 (mp0) cc_final: 0.6544 (mp0)
REVERT: B  207 LEU cc_start: 0.8034 (mt) cc_final: 0.7441 (mt)
REVERT: B  226 ASN cc_start: 0.8141 (m-40) cc_final: 0.7910 (m-40)
REVERT: B  227 HIS cc_start: 0.7681 (t-90) cc_final: 0.7393 (t-170)
REVERT: B  363 MET cc_start: 0.7860 (tpp) cc_final: 0.7639 (tpp)
REVERT: B  364 SER cc_start: 0.8809 (p) cc_final: 0.8405 (m)
REVERT: B  383 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7342 (mp0)
REVERT: B  406 MET cc_start: 0.9121 (mmm) cc_final: 0.8846 (mmm)
REVERT: C  244 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8321 (ptpt)
REVERT: C  250 PHE cc_start: 0.8517 (m-10) cc_final: 0.8275 (m-10)
REVERT: C  312 ASP cc_start: 0.8830 (m-30) cc_final: 0.8612 (m-30)
  outliers start: 35
  outliers final: 30
  residues processed: 162
  average time/residue: 0.0535
  time to fit residues: 12.5951
Evaluate side-chains
  160 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0570
   chunk 50 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.8104

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.135401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.101381 restraints weight = 16219.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.105583 restraints weight = 8668.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.108071 restraints weight = 6222.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.109587 restraints weight = 5184.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.110474 restraints weight = 4660.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   7839  Z= 0.195
  Angle     :  0.664  12.288  10619  Z= 0.344
  Chirality :  0.044   0.152   1158
  Planarity :  0.004   0.071   1396
  Dihedral  :  4.149  15.861   1055
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.92 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.27), residues: 967
  helix:  0.58 (0.23), residues: 480
  sheet: -0.01 (0.47), residues: 121
  loop : -0.28 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 282 
 TYR   0.038   0.002   TYR A  24 
 PHE   0.022   0.002   PHE B 270 
 TRP   0.028   0.002   TRP C 311 
 HIS   0.008   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 7839)
  covalent geometry    : angle       0.66447 (10619)
  hydrogen bonds       : bond        0.03953 (  421)
  hydrogen bonds       : angle       4.90103 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8394 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  199 ASP cc_start: 0.8091 (t0) cc_final: 0.7800 (t0)
REVERT: A  207 GLU cc_start: 0.7734 (mp0) cc_final: 0.7116 (mp0)
REVERT: A  213 CYS cc_start: 0.8718 (t) cc_final: 0.8413 (t)
REVERT: A  224 TYR cc_start: 0.3447 (OUTLIER) cc_final: 0.1293 (m-80)
REVERT: A  228 ASN cc_start: 0.8278 (m110) cc_final: 0.7955 (m110)
REVERT: A  313 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6450 (tmm)
REVERT: A  351 PHE cc_start: 0.6405 (p90) cc_final: 0.6000 (p90)
REVERT: B    1 MET cc_start: 0.7506 (mmt) cc_final: 0.7064 (pmm)
REVERT: B   16 ILE cc_start: 0.8147 (mp) cc_final: 0.7874 (mp)
REVERT: B   19 LYS cc_start: 0.9019 (tptm) cc_final: 0.8723 (tppt)
REVERT: B   73 MET cc_start: 0.5310 (mpt) cc_final: 0.4783 (mpp)
REVERT: B  181 GLU cc_start: 0.7630 (mp0) cc_final: 0.7347 (mp0)
REVERT: B  207 LEU cc_start: 0.8073 (mt) cc_final: 0.7497 (mt)
REVERT: B  226 ASN cc_start: 0.8172 (m-40) cc_final: 0.7811 (m110)
REVERT: B  227 HIS cc_start: 0.7831 (t-90) cc_final: 0.7611 (t-170)
REVERT: B  363 MET cc_start: 0.7929 (tpp) cc_final: 0.7672 (tpp)
REVERT: B  364 SER cc_start: 0.8813 (p) cc_final: 0.8403 (m)
REVERT: B  383 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7358 (mp0)
REVERT: B  389 PHE cc_start: 0.8174 (t80) cc_final: 0.7952 (m-80)
REVERT: B  406 MET cc_start: 0.9083 (mmm) cc_final: 0.8850 (mmm)
REVERT: C  250 PHE cc_start: 0.8586 (m-10) cc_final: 0.8347 (m-10)
REVERT: C  312 ASP cc_start: 0.8957 (m-30) cc_final: 0.8731 (m-30)
  outliers start: 31
  outliers final: 27
  residues processed: 159
  average time/residue: 0.0544
  time to fit residues: 12.5441
Evaluate side-chains
  156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.135324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.104129 restraints weight = 16061.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.105269 restraints weight = 8939.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.106629 restraints weight = 7251.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.106932 restraints weight = 6832.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.107211 restraints weight = 6201.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7839  Z= 0.158
  Angle     :  0.687  12.608  10619  Z= 0.343
  Chirality :  0.044   0.225   1158
  Planarity :  0.004   0.071   1396
  Dihedral  :  4.093  17.351   1055
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.28 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.27), residues: 967
  helix:  0.57 (0.23), residues: 481
  sheet:  0.07 (0.47), residues: 119
  loop : -0.31 (0.35), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 282 
 TYR   0.039   0.001   TYR A  24 
 PHE   0.028   0.002   PHE B 317 
 TRP   0.028   0.002   TRP C 311 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7839)
  covalent geometry    : angle       0.68746 (10619)
  hydrogen bonds       : bond        0.03731 (  421)
  hydrogen bonds       : angle       4.86781 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8387 (m-30) cc_final: 0.8128 (m-30)
REVERT: A  186 ASN cc_start: 0.7795 (p0) cc_final: 0.7501 (p0)
REVERT: A  207 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7400 (mp0)
REVERT: A  213 CYS cc_start: 0.8883 (t) cc_final: 0.8542 (t)
REVERT: A  224 TYR cc_start: 0.3427 (OUTLIER) cc_final: 0.1256 (m-80)
REVERT: A  228 ASN cc_start: 0.8314 (m110) cc_final: 0.7984 (m110)
REVERT: A  313 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6255 (tmm)
REVERT: A  351 PHE cc_start: 0.6547 (p90) cc_final: 0.6044 (p90)
REVERT: B    1 MET cc_start: 0.7456 (mmt) cc_final: 0.7074 (pmm)
REVERT: B   16 ILE cc_start: 0.8039 (mp) cc_final: 0.7777 (mp)
REVERT: B   19 LYS cc_start: 0.9039 (tptm) cc_final: 0.8749 (tppt)
REVERT: B   73 MET cc_start: 0.5542 (mpt) cc_final: 0.4993 (mpp)
REVERT: B  227 HIS cc_start: 0.7769 (t-90) cc_final: 0.7519 (t-170)
REVERT: B  364 SER cc_start: 0.8821 (p) cc_final: 0.8424 (m)
REVERT: C  250 PHE cc_start: 0.8642 (m-10) cc_final: 0.8405 (m-10)
REVERT: C  312 ASP cc_start: 0.8968 (m-30) cc_final: 0.8740 (m-30)
REVERT: C  313 MET cc_start: 0.8527 (ptp) cc_final: 0.7994 (ptp)
  outliers start: 31
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0551
  time to fit residues: 12.2512
Evaluate side-chains
  156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 89 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.135604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.104414 restraints weight = 15971.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.105844 restraints weight = 8920.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.106616 restraints weight = 7161.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.107741 restraints weight = 6849.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.108094 restraints weight = 6321.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7839  Z= 0.149
  Angle     :  0.707  12.690  10619  Z= 0.350
  Chirality :  0.043   0.177   1158
  Planarity :  0.004   0.083   1396
  Dihedral  :  4.073  16.463   1055
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.04 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.27), residues: 967
  helix:  0.51 (0.22), residues: 480
  sheet:  0.02 (0.47), residues: 119
  loop : -0.31 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 282 
 TYR   0.030   0.001   TYR A  24 
 PHE   0.025   0.002   PHE B 270 
 TRP   0.027   0.002   TRP C 311 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7839)
  covalent geometry    : angle       0.70692 (10619)
  hydrogen bonds       : bond        0.03787 (  421)
  hydrogen bonds       : angle       4.89557 ( 1218)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8393 (m-30) cc_final: 0.8115 (m-30)
REVERT: A  186 ASN cc_start: 0.7777 (p0) cc_final: 0.7349 (p0)
REVERT: A  207 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7396 (mp0)
REVERT: A  213 CYS cc_start: 0.8860 (t) cc_final: 0.8518 (t)
REVERT: A  224 TYR cc_start: 0.3324 (OUTLIER) cc_final: 0.1155 (m-80)
REVERT: A  228 ASN cc_start: 0.8341 (m110) cc_final: 0.8016 (m110)
REVERT: A  313 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6217 (tmm)
REVERT: A  351 PHE cc_start: 0.6523 (p90) cc_final: 0.5992 (p90)
REVERT: B    1 MET cc_start: 0.7438 (mmt) cc_final: 0.7052 (pmm)
REVERT: B   16 ILE cc_start: 0.8037 (mp) cc_final: 0.7557 (mp)
REVERT: B   19 LYS cc_start: 0.9008 (tptm) cc_final: 0.8725 (tppt)
REVERT: B   73 MET cc_start: 0.5618 (mpt) cc_final: 0.5111 (mpp)
REVERT: B  207 LEU cc_start: 0.7965 (mt) cc_final: 0.7405 (mt)
REVERT: B  226 ASN cc_start: 0.8141 (m-40) cc_final: 0.7667 (m110)
REVERT: B  227 HIS cc_start: 0.7591 (t-90) cc_final: 0.7369 (t-170)
REVERT: B  364 SER cc_start: 0.8687 (p) cc_final: 0.8404 (m)
REVERT: B  389 PHE cc_start: 0.8166 (t80) cc_final: 0.7946 (m-80)
REVERT: C  250 PHE cc_start: 0.8645 (m-10) cc_final: 0.8435 (m-10)
REVERT: C  252 TRP cc_start: 0.7719 (m100) cc_final: 0.7500 (m100)
REVERT: C  281 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6662 (tt0)
REVERT: C  282 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.8030 (tpp-160)
REVERT: C  301 GLU cc_start: 0.5610 (pm20) cc_final: 0.5336 (pm20)
REVERT: C  312 ASP cc_start: 0.8954 (m-30) cc_final: 0.8733 (m-30)
  outliers start: 29
  outliers final: 23
  residues processed: 154
  average time/residue: 0.0506
  time to fit residues: 11.4772
Evaluate side-chains
  156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.136197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.105026 restraints weight = 16071.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.106231 restraints weight = 9001.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.107664 restraints weight = 7167.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.108280 restraints weight = 6776.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.108345 restraints weight = 6218.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7839  Z= 0.141
  Angle     :  0.716  13.601  10619  Z= 0.355
  Chirality :  0.044   0.179   1158
  Planarity :  0.004   0.069   1396
  Dihedral  :  4.047  16.415   1055
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.40 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.27), residues: 967
  helix:  0.45 (0.22), residues: 480
  sheet:  0.08 (0.47), residues: 119
  loop : -0.28 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 282 
 TYR   0.032   0.001   TYR A  24 
 PHE   0.024   0.002   PHE C 286 
 TRP   0.030   0.002   TRP C 311 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7839)
  covalent geometry    : angle       0.71622 (10619)
  hydrogen bonds       : bond        0.03695 (  421)
  hydrogen bonds       : angle       4.87825 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1106.09 seconds
wall clock time: 19 minutes 54.86 seconds (1194.86 seconds total)