Starting phenix.real_space_refine
on Tue Feb 11 15:37:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vq5_32086/02_2025/7vq5_32086.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4074      2.51       5
     N    1052      2.21       5
     O    1155      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6315
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3153
          Classifications: {'peptide': 400}
          Link IDs: {'PTRANS': 12, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'LMR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.23, per 1000 atoms: 0.67
  Number of scatterers: 6315
  At special positions: 0
  Unit cell: (83.148, 90.246, 112.554, 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      34     16.00
     O    1155      8.00
     N    1052      7.00
     C    4074      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: 1.52
  Conformation dependent library (CDL) restraints added in 898.2 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 18
      removed outlier: 3.609A  pdb=" N   ASP A  18 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.942A  pdb=" N   GLY A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
    Processing helix  chain 'A' and resid 69 through 102
      removed outlier: 3.819A  pdb=" N   THR A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 125
      removed outlier: 4.587A  pdb=" N   ILE A 108 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 133
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.716A  pdb=" N   ILE A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 183
    Processing helix  chain 'A' and resid 187 through 214
    Processing helix  chain 'A' and resid 223 through 241
      removed outlier: 5.024A  pdb=" N   ARG A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   TYR A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP A 241 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 3.855A  pdb=" N   GLU A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 256 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 293
      removed outlier: 3.541A  pdb=" N   TYR A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.819A  pdb=" N   LYS A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 330
    Processing helix  chain 'A' and resid 335 through 357
      removed outlier: 4.400A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER A 344 " --> pdb=" O   HIS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
      removed outlier: 4.332A  pdb=" N   ASP A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 359 through 363'
    Processing helix  chain 'A' and resid 364 through 398
    Processing helix  chain 'B' and resid 2 through 18
      removed outlier: 3.518A  pdb=" N   ILE B   7 " --> pdb=" O   LYS B   3 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B  10 " --> pdb=" O   GLU B   6 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP B  18 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 39
      removed outlier: 3.543A  pdb=" N   ILE B  23 " --> pdb=" O   PRO B  19 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLY B  29 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.523A  pdb=" N   VAL B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 102
      removed outlier: 3.893A  pdb=" N   THR B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   HIS B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG B  99 " --> pdb=" O   HIS B  95 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 125
      removed outlier: 4.046A  pdb=" N   VAL B 111 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 133
      removed outlier: 4.026A  pdb=" N   THR B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B 133 " --> pdb=" O   TRP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 149
      removed outlier: 3.549A  pdb=" N   ILE B 138 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 145 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 183
      removed outlier: 3.715A  pdb=" N   MET B 159 " --> pdb=" O   ASP B 155 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B 163 " --> pdb=" O   MET B 159 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 171 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLY B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   CYS B 176 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 179 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 215
      removed outlier: 3.812A  pdb=" N   ASP B 201 " --> pdb=" O   ALA B 197 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE B 206 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASP B 212 " --> pdb=" O   GLN B 208 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B 215 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 241
      removed outlier: 4.884A  pdb=" N   ARG B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 240 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP B 241 " --> pdb=" O   LYS B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 256
      removed outlier: 3.657A  pdb=" N   GLU B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU B 254 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   TRP B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU B 256 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 291
      removed outlier: 3.512A  pdb=" N   GLN B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.665A  pdb=" N   LYS B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 330
      removed outlier: 3.881A  pdb=" N   GLU B 323 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 357
      removed outlier: 4.307A  pdb=" N   ILE B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN B 343 " --> pdb=" O   ILE B 339 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER B 344 " --> pdb=" O   HIS B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 363
      removed outlier: 4.277A  pdb=" N   ASP B 362 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL B 363 " --> pdb=" O   LEU B 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 359 through 363'
    Processing helix  chain 'B' and resid 364 through 396
      removed outlier: 4.667A  pdb=" N   SER B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B 387 " --> pdb=" O   ASN B 383 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1446 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1586
        1.33 -     1.45: 1178
        1.45 -     1.57: 3618
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" C1  LMR B 601 "
       pdb=" C2  LMR B 601 "
    ideal  model  delta    sigma   weight residual
    1.543  1.495  0.048 2.00e-02 2.50e+03 5.70e+00
  bond pdb=" C   ILE B  53 "
       pdb=" O   ILE B  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.212  0.025 1.19e-02 7.06e+03 4.27e+00
  bond pdb=" C   ILE A  53 "
       pdb=" O   ILE A  53 "
    ideal  model  delta    sigma   weight residual
    1.236  1.212  0.024 1.19e-02 7.06e+03 4.09e+00
  bond pdb=" CB  THR A 168 "
       pdb=" CG2 THR A 168 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.09e+00
  bond pdb=" C3  LMR B 601 "
       pdb=" C4  LMR B 601 "
    ideal  model  delta    sigma   weight residual
    1.538  1.503  0.035 2.00e-02 2.50e+03 3.07e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8187
        1.47 -     2.94: 453
        2.94 -     4.42: 47
        4.42 -     5.89: 7
        5.89 -     7.36: 8
  Bond angle restraints: 8702
  Sorted by residual:
  angle pdb=" C   GLU A 307 "
        pdb=" N   THR A 308 "
        pdb=" CA  THR A 308 "
      ideal   model   delta    sigma   weight residual
     119.83  116.03    3.80 1.11e+00 8.12e-01 1.17e+01
  angle pdb=" N   TYR A  39 "
        pdb=" CA  TYR A  39 "
        pdb=" C   TYR A  39 "
      ideal   model   delta    sigma   weight residual
     111.36  114.89   -3.53 1.09e+00 8.42e-01 1.05e+01
  angle pdb=" C   GLU B   6 "
        pdb=" N   ILE B   7 "
        pdb=" CA  ILE B   7 "
      ideal   model   delta    sigma   weight residual
     122.35  118.75    3.60 1.18e+00 7.18e-01 9.31e+00
  angle pdb=" C   THR A 132 "
        pdb=" N   LYS A 133 "
        pdb=" CA  LYS A 133 "
      ideal   model   delta    sigma   weight residual
     122.42  118.05    4.37 1.55e+00 4.16e-01 7.96e+00
  angle pdb=" C   GLY B 260 "
        pdb=" N   GLN B 261 "
        pdb=" CA  GLN B 261 "
      ideal   model   delta    sigma   weight residual
     124.31  128.72   -4.41 1.67e+00 3.59e-01 6.98e+00
  ... (remaining 8697 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3384
       17.98 -    35.95: 405
       35.95 -    53.93: 68
       53.93 -    71.91: 5
       71.91 -    89.89: 1
  Dihedral angle restraints: 3863
    sinusoidal: 1539
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  PRO A 299 "
           pdb=" C   PRO A 299 "
           pdb=" N   VAL A 300 "
           pdb=" CA  VAL A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.85  -23.15     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  TRP A 255 "
           pdb=" C   TRP A 255 "
           pdb=" N   GLU A 256 "
           pdb=" CA  GLU A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.40  -18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  LEU A 233 "
           pdb=" C   LEU A 233 "
           pdb=" N   GLU A 234 "
           pdb=" CA  GLU A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.11  -16.89     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 3860 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 783
       0.054 -    0.108: 197
       0.108 -    0.163: 15
       0.163 -    0.217: 1
       0.217 -    0.271: 1
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" CA  TYR A  39 "
            pdb=" N   TYR A  39 "
            pdb=" C   TYR A  39 "
            pdb=" CB  TYR A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  TYR A  40 "
            pdb=" N   TYR A  40 "
            pdb=" C   TYR A  40 "
            pdb=" CB  TYR A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  PRO B 258 "
            pdb=" N   PRO B 258 "
            pdb=" C   PRO B 258 "
            pdb=" CB  PRO B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.97e-01
  ... (remaining 994 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 257 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO B 258 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 258 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 258 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  18 "    0.028 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO A  19 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A  19 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  19 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 200 "   -0.013 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE B 200 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 200 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 200 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 200 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 200 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 200 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 97
        2.67 -     3.23: 6464
        3.23 -     3.78: 9458
        3.78 -     4.34: 12794
        4.34 -     4.90: 21454
  Nonbonded interactions: 50267
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" OD1 ASP B 286 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OE1 GLU B 246 "
            pdb=" NH2 ARG B 279 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" O   ILE B 369 "
            pdb=" OG1 THR B 373 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NH2 ARG B  80 "
            pdb=" O4A LMR B 601 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" NZ  LYS B 133 "
            pdb=" OE1 GLU B 254 "
     model   vdw
     2.247 3.120
  ... (remaining 50262 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 1 through 405)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.720
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
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      :  0.009   0.067   6442  Z= 0.599
  Angle     :  0.766   7.360   8702  Z= 0.446
  Chirality :  0.046   0.271    997
  Planarity :  0.004   0.043   1092
  Dihedral  : 14.845  89.886   2359
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 12.36 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.25), residues: 792
  helix: -1.79 (0.17), residues: 664
  sheet:  None (None), residues: 0
  loop : -4.38 (0.42), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 255 
 HIS   0.006   0.002   HIS B 259 
 PHE   0.023   0.002   PHE B 200 
 TYR   0.015   0.002   TYR A 271 
 ARG   0.005   0.001   ARG B 312 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.6907 (t-90)
REVERT: A  228 LYS cc_start: 0.7209 (pttt) cc_final: 0.6790 (pttt)
REVERT: A  368 MET cc_start: 0.7920 (mmm) cc_final: 0.7591 (mmm)
REVERT: A  372 MET cc_start: 0.8479 (mmm) cc_final: 0.8169 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2094
  time to fit residues: 25.6520
Evaluate side-chains
  77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 266 HIS
A 293 ASN
A 340 HIS
A 383 ASN
B 266 HIS
B 289 ASN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.139104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.101439 restraints weight = 8333.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.26
r_work: 0.3122 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6442  Z= 0.184
  Angle     :  0.506   5.599   8702  Z= 0.282
  Chirality :  0.038   0.143    997
  Planarity :  0.004   0.035   1092
  Dihedral  :  4.795  53.246    867
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.65 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.29), residues: 792
  helix:  0.41 (0.19), residues: 674
  sheet:  None (None), residues: 0
  loop : -3.94 (0.47), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 255 
 HIS   0.004   0.001   HIS B 193 
 PHE   0.015   0.001   PHE A 206 
 TYR   0.017   0.002   TYR A  39 
 ARG   0.003   0.000   ARG A 400 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7048 (t-90)
REVERT: A  228 LYS cc_start: 0.6771 (pttt) cc_final: 0.6447 (pttt)
REVERT: A  331 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.7616 (mpp)
REVERT: A  372 MET cc_start: 0.8821 (mmm) cc_final: 0.8370 (mmm)
REVERT: B   10 GLU cc_start: 0.8198 (tp30) cc_final: 0.7972 (tp30)
REVERT: B   17 GLU cc_start: 0.8163 (tt0) cc_final: 0.7942 (tt0)
REVERT: B  209 ASP cc_start: 0.7962 (m-30) cc_final: 0.7702 (m-30)
REVERT: B  228 LYS cc_start: 0.7359 (mttm) cc_final: 0.6753 (pttt)
REVERT: B  312 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8312 (tpp80)
  outliers start: 10
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1863
  time to fit residues: 25.4794
Evaluate side-chains
  92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue  331 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    0.1980
   chunk 31 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 64 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN
A 393 HIS
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.142448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.104949 restraints weight = 8606.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.25
r_work: 0.3193 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6442  Z= 0.190
  Angle     :  0.470   4.946   8702  Z= 0.257
  Chirality :  0.037   0.145    997
  Planarity :  0.003   0.037   1092
  Dihedral  :  4.570  54.641    867
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.24 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.30), residues: 792
  helix:  1.26 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -3.51 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.007   0.001   HIS A 393 
 PHE   0.015   0.001   PHE A 206 
 TYR   0.017   0.002   TYR A  39 
 ARG   0.002   0.000   ARG A 400 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7103 (t-90)
REVERT: A  228 LYS cc_start: 0.6873 (pttt) cc_final: 0.6553 (pttt)
REVERT: A  331 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7655 (mpp)
REVERT: A  372 MET cc_start: 0.8815 (mmm) cc_final: 0.8387 (mmm)
REVERT: B   40 TYR cc_start: 0.8826 (t80) cc_final: 0.8622 (t80)
REVERT: B  209 ASP cc_start: 0.7875 (m-30) cc_final: 0.7636 (m-30)
REVERT: B  228 LYS cc_start: 0.7283 (mttm) cc_final: 0.6741 (pttt)
REVERT: B  312 ARG cc_start: 0.8724 (tpp-160) cc_final: 0.8489 (tpp80)
  outliers start: 10
  outliers final: 5
  residues processed: 103
  average time/residue: 0.1739
  time to fit residues: 24.4432
Evaluate side-chains
  95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.137110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.099658 restraints weight = 8750.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.23
r_work: 0.3111 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6442  Z= 0.327
  Angle     :  0.535   6.164   8702  Z= 0.291
  Chirality :  0.039   0.139    997
  Planarity :  0.004   0.039   1092
  Dihedral  :  4.820  58.996    867
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.38 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.30), residues: 792
  helix:  1.47 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop : -3.45 (0.49), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 255 
 HIS   0.004   0.001   HIS A 193 
 PHE   0.013   0.002   PHE B 264 
 TYR   0.018   0.002   TYR A  39 
 ARG   0.003   0.000   ARG A  80 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7334 (t-90)
REVERT: A  228 LYS cc_start: 0.6979 (pttt) cc_final: 0.6624 (pttt)
REVERT: A  246 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: A  331 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.7730 (mpp)
REVERT: A  372 MET cc_start: 0.8807 (mmm) cc_final: 0.8470 (mmm)
REVERT: B  228 LYS cc_start: 0.7473 (mttm) cc_final: 0.6892 (pttt)
REVERT: B  312 ARG cc_start: 0.8771 (tpp-160) cc_final: 0.8446 (tpp80)
  outliers start: 20
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1871
  time to fit residues: 23.4686
Evaluate side-chains
  96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.142100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.104611 restraints weight = 8655.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.27
r_work: 0.3180 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6442  Z= 0.167
  Angle     :  0.457   5.456   8702  Z= 0.248
  Chirality :  0.036   0.145    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.531  58.458    867
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.39 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.31), residues: 792
  helix:  1.81 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.99 (0.53), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS B 193 
 PHE   0.014   0.001   PHE A 206 
 TYR   0.012   0.001   TYR A  39 
 ARG   0.003   0.000   ARG A 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7174 (t-90)
REVERT: A  228 LYS cc_start: 0.6820 (pttt) cc_final: 0.6505 (pttt)
REVERT: A  246 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8263 (mt-10)
REVERT: A  331 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.7733 (mpp)
REVERT: A  368 MET cc_start: 0.8142 (mmm) cc_final: 0.7512 (mmm)
REVERT: A  372 MET cc_start: 0.8753 (mmm) cc_final: 0.8225 (mmm)
REVERT: B   95 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7688 (t70)
REVERT: B  209 ASP cc_start: 0.7884 (m-30) cc_final: 0.7604 (m-30)
REVERT: B  228 LYS cc_start: 0.7281 (mttm) cc_final: 0.6765 (pttt)
REVERT: B  312 ARG cc_start: 0.8650 (tpp-160) cc_final: 0.8381 (tpp80)
  outliers start: 11
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1768
  time to fit residues: 23.6560
Evaluate side-chains
  100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 63 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.102731 restraints weight = 8620.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.25
r_work: 0.3161 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6442  Z= 0.220
  Angle     :  0.481   5.222   8702  Z= 0.259
  Chirality :  0.037   0.142    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.604  59.760    867
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.54 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.31), residues: 792
  helix:  1.92 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.92 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 255 
 HIS   0.005   0.001   HIS A 393 
 PHE   0.019   0.001   PHE A 206 
 TYR   0.013   0.002   TYR B  41 
 ARG   0.005   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7320 (t-90)
REVERT: A  228 LYS cc_start: 0.6860 (pttt) cc_final: 0.6544 (pttt)
REVERT: A  246 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: A  331 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7692 (mpp)
REVERT: A  372 MET cc_start: 0.8773 (mmm) cc_final: 0.8378 (mmm)
REVERT: B   95 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7710 (t70)
REVERT: B  209 ASP cc_start: 0.7893 (m-30) cc_final: 0.7624 (m-30)
REVERT: B  228 LYS cc_start: 0.7280 (mttm) cc_final: 0.6754 (pttt)
REVERT: B  312 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8386 (tpp80)
  outliers start: 16
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1761
  time to fit residues: 23.4243
Evaluate side-chains
  100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.105683 restraints weight = 8573.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.26
r_work: 0.3198 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6442  Z= 0.160
  Angle     :  0.448   5.516   8702  Z= 0.242
  Chirality :  0.036   0.144    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.443  59.675    867
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.11 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.30), residues: 792
  helix:  2.09 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.71 (0.56), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.005   0.001   HIS A 393 
 PHE   0.016   0.001   PHE A 206 
 TYR   0.013   0.001   TYR A  41 
 ARG   0.004   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7268 (t-90)
REVERT: A  228 LYS cc_start: 0.6790 (pttt) cc_final: 0.6491 (pttt)
REVERT: A  246 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8180 (mt-10)
REVERT: A  331 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.7725 (mpp)
REVERT: A  368 MET cc_start: 0.8158 (mmm) cc_final: 0.7551 (mmm)
REVERT: A  372 MET cc_start: 0.8699 (mmm) cc_final: 0.8149 (mmm)
REVERT: A  405 MET cc_start: 0.5433 (mmt) cc_final: 0.4898 (mmm)
REVERT: B   95 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7570 (t70)
REVERT: B  154 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6450 (mmm160)
REVERT: B  228 LYS cc_start: 0.7219 (mttm) cc_final: 0.6741 (pttt)
REVERT: B  312 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8394 (tpt170)
REVERT: B  313 MET cc_start: 0.8036 (mtt) cc_final: 0.7772 (mtp)
  outliers start: 15
  outliers final: 9
  residues processed: 105
  average time/residue: 0.1664
  time to fit residues: 24.2670
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 2 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   overall best weight:    0.9420

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.103720 restraints weight = 8370.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.26
r_work: 0.3181 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6442  Z= 0.162
  Angle     :  0.446   5.164   8702  Z= 0.241
  Chirality :  0.036   0.144    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.369  58.762    867
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 21.12 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.30), residues: 792
  helix:  2.22 (0.20), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.63 (0.56), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.005   0.001   HIS A 393 
 PHE   0.017   0.001   PHE B 153 
 TYR   0.016   0.002   TYR A  41 
 ARG   0.003   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7264 (t-90)
REVERT: A  228 LYS cc_start: 0.6619 (pttt) cc_final: 0.6356 (pttt)
REVERT: A  246 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8181 (mt-10)
REVERT: A  331 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7740 (mpp)
REVERT: A  368 MET cc_start: 0.8124 (mmm) cc_final: 0.7486 (mmm)
REVERT: A  372 MET cc_start: 0.8636 (mmm) cc_final: 0.8050 (mmm)
REVERT: A  405 MET cc_start: 0.5500 (mmt) cc_final: 0.4965 (mmm)
REVERT: B   95 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7474 (t70)
REVERT: B  154 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6250 (mmm160)
REVERT: B  228 LYS cc_start: 0.7062 (mttm) cc_final: 0.6618 (pttt)
REVERT: B  312 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8186 (tpt170)
REVERT: B  368 MET cc_start: 0.7788 (tpp) cc_final: 0.7449 (tpp)
REVERT: B  405 MET cc_start: 0.5409 (mmp) cc_final: 0.4503 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1672
  time to fit residues: 22.9456
Evaluate side-chains
  104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  241 ASP
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.105135 restraints weight = 8466.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.27
r_work: 0.3175 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6442  Z= 0.150
  Angle     :  0.441   6.114   8702  Z= 0.236
  Chirality :  0.036   0.144    997
  Planarity :  0.003   0.039   1092
  Dihedral  :  4.304  58.209    867
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.70 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.30), residues: 792
  helix:  2.28 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -2.95 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.006   0.001   HIS A 393 
 PHE   0.020   0.001   PHE A 153 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.003   0.000   ARG B 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7322 (t-90)
REVERT: A  228 LYS cc_start: 0.6599 (pttt) cc_final: 0.6346 (pttt)
REVERT: A  246 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8183 (mt-10)
REVERT: A  331 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7720 (mpp)
REVERT: A  368 MET cc_start: 0.8066 (mmm) cc_final: 0.7444 (mmm)
REVERT: A  372 MET cc_start: 0.8586 (mmm) cc_final: 0.7974 (mmm)
REVERT: A  405 MET cc_start: 0.5573 (mmt) cc_final: 0.4946 (mmm)
REVERT: B   95 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7479 (t70)
REVERT: B  154 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6283 (mmm160)
REVERT: B  228 LYS cc_start: 0.7096 (mttm) cc_final: 0.6660 (pttt)
REVERT: B  312 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.7982 (tpt170)
REVERT: B  368 MET cc_start: 0.7767 (tpp) cc_final: 0.7396 (tpt)
REVERT: B  405 MET cc_start: 0.5577 (mmp) cc_final: 0.4630 (mmm)
  outliers start: 15
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1717
  time to fit residues: 24.3740
Evaluate side-chains
  104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.103701 restraints weight = 8472.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.25
r_work: 0.3155 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6442  Z= 0.185
  Angle     :  0.456   6.015   8702  Z= 0.245
  Chirality :  0.037   0.143    997
  Planarity :  0.003   0.038   1092
  Dihedral  :  4.352  56.844    867
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 22.13 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.30), residues: 792
  helix:  2.36 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -2.43 (0.53), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 255 
 HIS   0.006   0.001   HIS A 393 
 PHE   0.020   0.001   PHE A 153 
 TYR   0.015   0.001   TYR A  50 
 ARG   0.003   0.000   ARG A 235 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A   95 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7393 (t-90)
REVERT: A  228 LYS cc_start: 0.6742 (pttt) cc_final: 0.6478 (pttt)
REVERT: A  246 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: A  331 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7775 (mpp)
REVERT: A  368 MET cc_start: 0.8088 (mmm) cc_final: 0.7467 (mmm)
REVERT: A  372 MET cc_start: 0.8603 (mmm) cc_final: 0.7985 (mmm)
REVERT: A  405 MET cc_start: 0.5648 (mmt) cc_final: 0.5014 (mmm)
REVERT: B   10 GLU cc_start: 0.8057 (tp30) cc_final: 0.7698 (tp30)
REVERT: B   95 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7496 (t70)
REVERT: B  154 ARG cc_start: 0.7147 (mtp85) cc_final: 0.6277 (mmm160)
REVERT: B  228 LYS cc_start: 0.7085 (mttm) cc_final: 0.6637 (pttt)
REVERT: B  312 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.8008 (tpp80)
REVERT: B  368 MET cc_start: 0.7793 (tpp) cc_final: 0.7405 (tpt)
REVERT: B  405 MET cc_start: 0.5498 (mmp) cc_final: 0.4558 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1704
  time to fit residues: 23.0048
Evaluate side-chains
  104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   95 HIS
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 393 HIS
B 340 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.142217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.104254 restraints weight = 8604.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.28
r_work: 0.3170 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6442  Z= 0.165
  Angle     :  0.446   6.305   8702  Z= 0.239
  Chirality :  0.036   0.144    997
  Planarity :  0.003   0.038   1092
  Dihedral  :  4.284  56.405    867
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 22.27 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.30), residues: 792
  helix:  2.38 (0.20), residues: 676
  sheet:  None (None), residues: 0
  loop : -2.80 (0.50), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 255 
 HIS   0.006   0.001   HIS A 393 
 PHE   0.018   0.001   PHE A 153 
 TYR   0.015   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B 312 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3322.02 seconds
wall clock time: 59 minutes 40.31 seconds (3580.31 seconds total)