Starting phenix.real_space_refine
on Tue Feb  3 17:42:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lgt_63072/02_2026/9lgt_63072.map"
  }
  resolution = 3.68
  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=   0.001 sd=   0.022
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      28      5.16       5
     C    3732      2.51       5
     N     914      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5650
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2825
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 17, 'TRANS': 364}
    Chain: "B"
      Number of atoms: 2825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2825
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 17, 'TRANS': 364}
  Time building chain proxies: 1.22, per 1000 atoms: 0.22
  Number of scatterers: 5650
  At special positions: 0
  Unit cell: (96.86, 95.524, 69.472, 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      28     16.00
     O     976      8.00
     N     914      7.00
     C    3732      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 254 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 254 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 312.5 milliseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 2 sheets defined
      85.1% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 40
      removed outlier: 4.052A  pdb=" N   LEU A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 46
      removed outlier: 4.115A  pdb=" N   VAL A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   VAL A  46 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 58
      removed outlier: 4.223A  pdb=" N   ALA A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 81
      removed outlier: 3.551A  pdb=" N   SER A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   GLN A  74 " --> pdb=" O   HIS A  70 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   VAL A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 95
      removed outlier: 3.546A  pdb=" N   PHE A  95 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 125
      removed outlier: 3.524A  pdb=" N   GLY A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 150
      removed outlier: 3.574A  pdb=" N   GLY A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 174 through 204
      removed outlier: 3.775A  pdb=" N   GLY A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TRP A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 205 through 221
      removed outlier: 3.515A  pdb=" N   ALA A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 224
      No H-bonds generated for 'chain 'A' and resid 222 through 224'
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 3.579A  pdb=" N   TRP A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 250 through 258
    Processing helix  chain 'A' and resid 259 through 266
    Processing helix  chain 'A' and resid 267 through 273
      removed outlier: 4.520A  pdb=" N   GLY A 270 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   GLN A 271 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   LEU A 272 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 267 through 273'
    Processing helix  chain 'A' and resid 274 through 281
      removed outlier: 4.109A  pdb=" N   PHE A 278 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 294
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'A' and resid 298 through 317
    Processing helix  chain 'A' and resid 319 through 328
      removed outlier: 4.273A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   PHE A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   PHE A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'A' and resid 362 through 369
    Processing helix  chain 'A' and resid 370 through 373
    Processing helix  chain 'A' and resid 375 through 402
      removed outlier: 3.515A  pdb=" N   LEU A 401 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 40
    Processing helix  chain 'B' and resid 40 through 45
      removed outlier: 4.269A  pdb=" N   VAL B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 59
      removed outlier: 4.261A  pdb=" N   ALA B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 82
      removed outlier: 3.710A  pdb=" N   SER B  69 " --> pdb=" O   PRO B  65 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   HIS B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLY B  81 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN B  82 " --> pdb=" O   SER B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 95
      removed outlier: 3.504A  pdb=" N   PHE B  95 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 3.525A  pdb=" N   GLY B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 150
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'B' and resid 167 through 204
      removed outlier: 4.101A  pdb=" N   PHE B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TRP B 187 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      Proline residue:  B 188  - end of helix
    Processing helix  chain 'B' and resid 205 through 221
      removed outlier: 3.916A  pdb=" N   SER B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 237
      removed outlier: 3.602A  pdb=" N   TRP B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
      Proline residue:  B 232  - end of helix
      removed outlier: 4.006A  pdb=" N   ALA B 237 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 258
    Processing helix  chain 'B' and resid 259 through 266
    Processing helix  chain 'B' and resid 267 through 273
      removed outlier: 4.510A  pdb=" N   GLY B 270 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   GLN B 271 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   LEU B 272 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B 273 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 267 through 273'
    Processing helix  chain 'B' and resid 274 through 281
      removed outlier: 4.078A  pdb=" N   PHE B 278 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 294
      removed outlier: 3.543A  pdb=" N   ALA B 285 " --> pdb=" O   PHE B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 297
      No H-bonds generated for 'chain 'B' and resid 295 through 297'
    Processing helix  chain 'B' and resid 298 through 316
    Processing helix  chain 'B' and resid 319 through 327
      removed outlier: 4.223A  pdb=" N   ALA B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE B 326 " --> pdb=" O   ILE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 352
    Processing helix  chain 'B' and resid 362 through 369
    Processing helix  chain 'B' and resid 370 through 373
    Processing helix  chain 'B' and resid 375 through 402
    Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241

    404 hydrogen bonds defined for protein.
    1188 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: 0.57

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 929
        1.32 -     1.44: 1571
        1.44 -     1.57: 3248
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 5798
  Sorted by residual:
  bond pdb=" CA  TYR B 386 "
       pdb=" C   TYR B 386 "
    ideal  model  delta    sigma   weight residual
    1.524  1.438  0.086 1.29e-02 6.01e+03 4.42e+01
  bond pdb=" CA  ILE B 398 "
       pdb=" C   ILE B 398 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.074 1.27e-02 6.20e+03 3.40e+01
  bond pdb=" CA  ILE A 398 "
       pdb=" C   ILE A 398 "
    ideal  model  delta    sigma   weight residual
    1.523  1.449  0.074 1.27e-02 6.20e+03 3.38e+01
  bond pdb=" CA  TYR A 386 "
       pdb=" C   TYR A 386 "
    ideal  model  delta    sigma   weight residual
    1.524  1.450  0.074 1.29e-02 6.01e+03 3.27e+01
  bond pdb=" C   TYR B 386 "
       pdb=" N   ALA B 387 "
    ideal  model  delta    sigma   weight residual
    1.335  1.284  0.051 1.31e-02 5.83e+03 1.53e+01
  ... (remaining 5793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 7567
        1.38 -     2.76: 251
        2.76 -     4.14: 58
        4.14 -     5.51: 21
        5.51 -     6.89: 7
  Bond angle restraints: 7904
  Sorted by residual:
  angle pdb=" N   ILE A 398 "
        pdb=" CA  ILE A 398 "
        pdb=" C   ILE A 398 "
      ideal   model   delta    sigma   weight residual
     110.62  105.34    5.28 1.02e+00 9.61e-01 2.68e+01
  angle pdb=" N   ILE B 398 "
        pdb=" CA  ILE B 398 "
        pdb=" C   ILE B 398 "
      ideal   model   delta    sigma   weight residual
     110.62  105.47    5.15 1.02e+00 9.61e-01 2.55e+01
  angle pdb=" C   TYR A 386 "
        pdb=" CA  TYR A 386 "
        pdb=" CB  TYR A 386 "
      ideal   model   delta    sigma   weight residual
     110.85  103.96    6.89 1.70e+00 3.46e-01 1.64e+01
  angle pdb=" C   TYR B 386 "
        pdb=" CA  TYR B 386 "
        pdb=" CB  TYR B 386 "
      ideal   model   delta    sigma   weight residual
     110.85  104.03    6.82 1.70e+00 3.46e-01 1.61e+01
  angle pdb=" N   TRP B 187 "
        pdb=" CA  TRP B 187 "
        pdb=" C   TRP B 187 "
      ideal   model   delta    sigma   weight residual
     109.81  116.49   -6.68 2.21e+00 2.05e-01 9.15e+00
  ... (remaining 7899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.97: 2982
       15.97 -    31.95: 226
       31.95 -    47.92: 56
       47.92 -    63.90: 10
       63.90 -    79.87: 4
  Dihedral angle restraints: 3278
    sinusoidal: 1158
      harmonic: 2120
  Sorted by residual:
  dihedral pdb=" CA  PHE B 359 "
           pdb=" C   PHE B 359 "
           pdb=" N   SER B 360 "
           pdb=" CA  SER B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.35  -18.65     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CB  MET B  83 "
           pdb=" CG  MET B  83 "
           pdb=" SD  MET B  83 "
           pdb=" CE  MET B  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.27  -57.73     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA  TRP A 187 "
           pdb=" C   TRP A 187 "
           pdb=" N   PRO A 188 "
           pdb=" CA  PRO A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.80  -15.20     0      5.00e+00 4.00e-02 9.24e+00
  ... (remaining 3275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 755
       0.067 -    0.135: 155
       0.135 -    0.202: 4
       0.202 -    0.270: 1
       0.270 -    0.337: 1
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CA  ARG A 399 "
            pdb=" N   ARG A 399 "
            pdb=" C   ARG A 399 "
            pdb=" CB  ARG A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  TYR A 276 "
            pdb=" N   TYR A 276 "
            pdb=" C   TYR A 276 "
            pdb=" CB  TYR A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  LEU B 401 "
            pdb=" N   LEU B 401 "
            pdb=" C   LEU B 401 "
            pdb=" CB  LEU B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 913 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  47 "   -0.041 5.00e-02 4.00e+02   6.18e-02 6.12e+00
        pdb=" N   PRO A  48 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  47 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO B  48 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B  48 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  48 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 390 "    0.014 2.00e-02 2.50e+03   1.38e-02 3.83e+00
        pdb=" CG  TYR A 390 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 390 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 390 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 390 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 390 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 390 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 390 "    0.001 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1104
        2.77 -     3.30: 5609
        3.30 -     3.83: 9422
        3.83 -     4.37: 10725
        4.37 -     4.90: 18832
  Nonbonded interactions: 45692
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 226 "
            pdb=" ND2 ASN A 230 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   ARG A 218 "
            pdb=" OH  TYR A 334 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OH  TYR B 276 "
            pdb=" O   GLY B 356 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   TYR A 345 "
            pdb=" ND2 ASN A 349 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" O   ARG B 218 "
            pdb=" OH  TYR B 334 "
     model   vdw
     2.346 3.040
  ... (remaining 45687 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.260
  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:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.830
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6796
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      :  0.005   0.086   5800  Z= 0.311
  Angle     :  0.666   6.892   7908  Z= 0.371
  Chirality :  0.051   0.337    916
  Planarity :  0.006   0.062   1000
  Dihedral  : 12.672  79.871   1936
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.70 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.31), residues: 760
  helix:  1.12 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.40 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.034   0.003   TYR A 390 
 PHE   0.015   0.002   PHE B  80 
 TRP   0.012   0.001   TRP A 229 
 HIS   0.005   0.002   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 5798)
  covalent geometry    : angle       0.66530 ( 7904)
  SS BOND              : bond        0.00881 (    2)
  SS BOND              : angle       1.22944 (    4)
  hydrogen bonds       : bond        0.13270 (  404)
  hydrogen bonds       : angle       6.61205 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8240 (mmm) cc_final: 0.7938 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 109
  average time/residue: 0.0523
  time to fit residues: 8.0352
Evaluate side-chains
  110 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain B residue  386 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130705 restraints weight = 8040.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.133534 restraints weight = 4850.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135474 restraints weight = 3284.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.136799 restraints weight = 2404.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.137704 restraints weight = 1862.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5800  Z= 0.184
  Angle     :  0.641   8.924   7908  Z= 0.333
  Chirality :  0.048   0.150    916
  Planarity :  0.006   0.063   1000
  Dihedral  :  5.217  59.490    804
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  7.92 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.30), residues: 760
  helix:  1.21 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.78 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 372 
 TYR   0.020   0.002   TYR A 390 
 PHE   0.018   0.001   PHE A 314 
 TRP   0.010   0.001   TRP A 229 
 HIS   0.005   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 5798)
  covalent geometry    : angle       0.63992 ( 7904)
  SS BOND              : bond        0.00662 (    2)
  SS BOND              : angle       1.47917 (    4)
  hydrogen bonds       : bond        0.05229 (  404)
  hydrogen bonds       : angle       5.42099 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  349 ASN cc_start: 0.7683 (m-40) cc_final: 0.7185 (m110)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.0609
  time to fit residues: 9.2425
Evaluate side-chains
  112 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.130963 restraints weight = 8015.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133805 restraints weight = 4852.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135745 restraints weight = 3279.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.137045 restraints weight = 2396.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.137955 restraints weight = 1858.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5800  Z= 0.166
  Angle     :  0.614  10.860   7908  Z= 0.318
  Chirality :  0.047   0.146    916
  Planarity :  0.006   0.064   1000
  Dihedral  :  4.244  20.092    800
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.04 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.30), residues: 760
  helix:  1.26 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.74 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 372 
 TYR   0.018   0.002   TYR A 390 
 PHE   0.023   0.001   PHE A 278 
 TRP   0.010   0.001   TRP A 229 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5798)
  covalent geometry    : angle       0.61304 ( 7904)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       1.35167 (    4)
  hydrogen bonds       : bond        0.04845 (  404)
  hydrogen bonds       : angle       5.25555 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8341 (tpp) cc_final: 0.8063 (tpt)
REVERT: A  345 TYR cc_start: 0.7956 (m-80) cc_final: 0.7411 (m-80)
REVERT: A  349 ASN cc_start: 0.7723 (m-40) cc_final: 0.7257 (m110)
  outliers start: 9
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0441
  time to fit residues: 6.9646
Evaluate side-chains
  115 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.144263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.132035 restraints weight = 7994.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134906 restraints weight = 4828.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.136858 restraints weight = 3268.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.138114 restraints weight = 2391.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.139134 restraints weight = 1879.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5800  Z= 0.139
  Angle     :  0.588  11.005   7908  Z= 0.303
  Chirality :  0.045   0.143    916
  Planarity :  0.006   0.065   1000
  Dihedral  :  4.108  19.749    800
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.91 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.31), residues: 760
  helix:  1.47 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 372 
 TYR   0.014   0.002   TYR A 390 
 PHE   0.012   0.001   PHE B 210 
 TRP   0.008   0.001   TRP A 229 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5798)
  covalent geometry    : angle       0.58763 ( 7904)
  SS BOND              : bond        0.00490 (    2)
  SS BOND              : angle       1.16982 (    4)
  hydrogen bonds       : bond        0.04450 (  404)
  hydrogen bonds       : angle       5.11612 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8374 (tpp) cc_final: 0.8053 (tpt)
  outliers start: 8
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0581
  time to fit residues: 8.6185
Evaluate side-chains
  108 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0000
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 298 ASN
B 349 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.143468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.131052 restraints weight = 8210.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133896 restraints weight = 4964.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.135942 restraints weight = 3353.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.137291 restraints weight = 2444.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138323 restraints weight = 1887.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5800  Z= 0.160
  Angle     :  0.603  11.918   7908  Z= 0.311
  Chirality :  0.046   0.143    916
  Planarity :  0.006   0.066   1000
  Dihedral  :  4.179  20.425    800
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.26 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.30), residues: 760
  helix:  1.40 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 372 
 TYR   0.013   0.002   TYR A 390 
 PHE   0.013   0.001   PHE A 366 
 TRP   0.008   0.001   TRP A 229 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5798)
  covalent geometry    : angle       0.60259 ( 7904)
  SS BOND              : bond        0.00561 (    2)
  SS BOND              : angle       1.20731 (    4)
  hydrogen bonds       : bond        0.04636 (  404)
  hydrogen bonds       : angle       5.12750 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.199 
Fit side-chains
  outliers start: 12
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0570
  time to fit residues: 8.4763
Evaluate side-chains
  110 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.130398 restraints weight = 8164.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133276 restraints weight = 4904.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135289 restraints weight = 3304.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.136673 restraints weight = 2403.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.137594 restraints weight = 1851.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5800  Z= 0.182
  Angle     :  0.619  12.035   7908  Z= 0.321
  Chirality :  0.047   0.144    916
  Planarity :  0.006   0.067   1000
  Dihedral  :  4.272  20.830    800
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.49 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.30), residues: 760
  helix:  1.27 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.016   0.002   TYR B 390 
 PHE   0.024   0.001   PHE A 278 
 TRP   0.007   0.001   TRP A 229 
 HIS   0.004   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 5798)
  covalent geometry    : angle       0.61805 ( 7904)
  SS BOND              : bond        0.00674 (    2)
  SS BOND              : angle       1.28253 (    4)
  hydrogen bonds       : bond        0.04841 (  404)
  hydrogen bonds       : angle       5.15936 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.7901 (m-80) cc_final: 0.7628 (m-80)
  outliers start: 12
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0590
  time to fit residues: 8.9843
Evaluate side-chains
  113 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0170
   chunk 42 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.144236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131816 restraints weight = 8156.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134655 restraints weight = 4910.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.136713 restraints weight = 3301.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.138093 restraints weight = 2405.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.139089 restraints weight = 1845.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5800  Z= 0.143
  Angle     :  0.604  12.943   7908  Z= 0.310
  Chirality :  0.045   0.144    916
  Planarity :  0.006   0.067   1000
  Dihedral  :  4.149  20.254    800
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.20 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.31), residues: 760
  helix:  1.42 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.011   0.002   TYR B 390 
 PHE   0.011   0.001   PHE B 210 
 TRP   0.009   0.001   TRP B 229 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5798)
  covalent geometry    : angle       0.60366 ( 7904)
  SS BOND              : bond        0.00534 (    2)
  SS BOND              : angle       1.21659 (    4)
  hydrogen bonds       : bond        0.04449 (  404)
  hydrogen bonds       : angle       5.06794 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.7843 (m-80) cc_final: 0.7581 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0629
  time to fit residues: 9.2401
Evaluate side-chains
  109 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.144316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.131977 restraints weight = 8029.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.134860 restraints weight = 4827.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136860 restraints weight = 3252.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.138169 restraints weight = 2367.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.139204 restraints weight = 1837.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5800  Z= 0.146
  Angle     :  0.606  13.623   7908  Z= 0.310
  Chirality :  0.046   0.143    916
  Planarity :  0.006   0.067   1000
  Dihedral  :  4.150  20.154    800
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.73 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.31), residues: 760
  helix:  1.40 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.48 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.012   0.002   TYR B 390 
 PHE   0.021   0.001   PHE A 278 
 TRP   0.010   0.001   TRP B 229 
 HIS   0.003   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5798)
  covalent geometry    : angle       0.60560 ( 7904)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       1.11493 (    4)
  hydrogen bonds       : bond        0.04453 (  404)
  hydrogen bonds       : angle       5.04788 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.7883 (m-80) cc_final: 0.7616 (m-80)
REVERT: B  386 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7698 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0721
  time to fit residues: 10.8040
Evaluate side-chains
  111 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  386 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0370
   chunk 43 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132115 restraints weight = 8031.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.134992 restraints weight = 4819.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136834 restraints weight = 3247.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138272 restraints weight = 2388.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.139293 restraints weight = 1838.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   5800  Z= 0.149
  Angle     :  0.618  14.005   7908  Z= 0.316
  Chirality :  0.046   0.152    916
  Planarity :  0.006   0.066   1000
  Dihedral  :  4.179  20.079    800
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.25 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.31), residues: 760
  helix:  1.41 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.45 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.012   0.002   TYR B 390 
 PHE   0.017   0.001   PHE B 278 
 TRP   0.011   0.001   TRP A 229 
 HIS   0.003   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5798)
  covalent geometry    : angle       0.61794 ( 7904)
  SS BOND              : bond        0.00544 (    2)
  SS BOND              : angle       1.08941 (    4)
  hydrogen bonds       : bond        0.04471 (  404)
  hydrogen bonds       : angle       5.06598 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  345 TYR cc_start: 0.7881 (m-80) cc_final: 0.7644 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0544
  time to fit residues: 8.1473
Evaluate side-chains
  108 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.143026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.130638 restraints weight = 8133.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133511 restraints weight = 4862.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.135454 restraints weight = 3284.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136861 restraints weight = 2393.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137867 restraints weight = 1843.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   5800  Z= 0.192
  Angle     :  0.643  14.007   7908  Z= 0.332
  Chirality :  0.048   0.159    916
  Planarity :  0.006   0.066   1000
  Dihedral  :  4.347  20.699    800
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.08 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 760
  helix:  1.18 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.46 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 372 
 TYR   0.014   0.002   TYR B 390 
 PHE   0.023   0.001   PHE A 278 
 TRP   0.009   0.001   TRP A 229 
 HIS   0.004   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 5798)
  covalent geometry    : angle       0.64297 ( 7904)
  SS BOND              : bond        0.00697 (    2)
  SS BOND              : angle       1.17453 (    4)
  hydrogen bonds       : bond        0.04822 (  404)
  hydrogen bonds       : angle       5.14155 ( 1188)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  402 ASN cc_start: 0.7907 (t0) cc_final: 0.7632 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0579
  time to fit residues: 9.0385
Evaluate side-chains
  113 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 40 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.144466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132438 restraints weight = 7912.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135247 restraints weight = 4773.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137208 restraints weight = 3225.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138533 restraints weight = 2346.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139497 restraints weight = 1805.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5800  Z= 0.145
  Angle     :  0.628  14.702   7908  Z= 0.320
  Chirality :  0.046   0.149    916
  Planarity :  0.006   0.064   1000
  Dihedral  :  4.254  20.190    800
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.61 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.31), residues: 760
  helix:  1.35 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.41 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.011   0.002   TYR B 390 
 PHE   0.017   0.001   PHE B 278 
 TRP   0.011   0.001   TRP B 229 
 HIS   0.003   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5798)
  covalent geometry    : angle       0.62719 ( 7904)
  SS BOND              : bond        0.00547 (    2)
  SS BOND              : angle       1.23237 (    4)
  hydrogen bonds       : bond        0.04508 (  404)
  hydrogen bonds       : angle       5.05987 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 962.87 seconds
wall clock time: 17 minutes 25.86 seconds (1045.86 seconds total)