Starting phenix.real_space_refine
on Thu Jun  5 11:40:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zke_60190/06_2025/8zke_60190_trim.cif"
  }
  resolution = 3.72
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    1988      2.51       5
     N     474      2.21       5
     O     505      1.98       5
     H    3070      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6057
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 6024
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 11, 'TRANS': 374}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'2YP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.24, per 1000 atoms: 0.70
  Number of scatterers: 6057
  At special positions: 0
  Unit cell: (75.472, 74.624, 73.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     O     505      8.00
     N     474      7.00
     C    1988      6.00
     H    3070      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 595.3 milliseconds
  

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  696

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      81.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 24
      removed outlier: 4.357A  pdb=" N   LEU A  18 " --> pdb=" O   SER A  14 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ILE A  19 " --> pdb=" O   ALA A  15 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA A  23 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 42
      removed outlier: 3.936A  pdb=" N   GLU A  42 " --> pdb=" O   TRP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 51
      removed outlier: 3.996A  pdb=" N   GLY A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 60
      removed outlier: 3.749A  pdb=" N   GLY A  56 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ALA A  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 3.697A  pdb=" N   MET A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   ASP A  70 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 70'
    Processing helix  chain 'A' and resid 82 through 101
      removed outlier: 3.709A  pdb=" N   THR A  86 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   LEU A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE A  93 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY A  99 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 4.061A  pdb=" N   ALA A 112 " --> pdb=" O   ARG A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 131
      removed outlier: 3.873A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 159
      removed outlier: 4.450A  pdb=" N   SER A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU A 150 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   GLY A 155 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 170
      removed outlier: 3.830A  pdb=" N   ALA A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   MET A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 183
      removed outlier: 4.188A  pdb=" N   MET A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 177 " --> pdb=" O   TRP A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 192
      removed outlier: 4.137A  pdb=" N   CYS A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.411A  pdb=" N   VAL A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A 212 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 218
      removed outlier: 3.929A  pdb=" N   ARG A 216 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 235
      removed outlier: 3.531A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LYS A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 3.628A  pdb=" N   PHE A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA A 241 " --> pdb=" O   GLY A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 251
      removed outlier: 3.660A  pdb=" N   ILE A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 260
      No H-bonds generated for 'chain 'A' and resid 258 through 260'
    Processing helix  chain 'A' and resid 261 through 266
    Processing helix  chain 'A' and resid 266 through 285
      removed outlier: 3.997A  pdb=" N   VAL A 281 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 298
      removed outlier: 4.236A  pdb=" N   LEU A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 3.584A  pdb=" N   ASN A 303 " --> pdb=" O   GLN A 299 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   GLY A 305 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   TYR A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TRP A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 311 " --> pdb=" O   TRP A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 345
      removed outlier: 3.524A  pdb=" N   PHE A 324 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASN A 327 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 330 " --> pdb=" O   GLU A 326 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ALA A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ALA A 336 " --> pdb=" O   MET A 332 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   CYS A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 379
      removed outlier: 3.505A  pdb=" N   PHE A 354 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU A 356 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 357 " --> pdb=" O   GLN A 353 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLY A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   ARG A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   GLY A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
      removed outlier: 3.609A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA A 378 " --> pdb=" O   TRP A 374 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   HIS A 379 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 387
      removed outlier: 3.518A  pdb=" N   PHE A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 403
      removed outlier: 3.762A  pdb=" N   LEU A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ILE A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.828A  pdb=" N   TYR A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 409 " --> pdb=" O   THR A 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 409'

    139 hydrogen bonds defined for protein.
    396 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 3065
        1.04 -     1.23: 65
        1.23 -     1.43: 1213
        1.43 -     1.62: 1754
        1.62 -     1.82: 35
  Bond restraints: 6132
  Sorted by residual:
  bond pdb=" CA5 2YP A 501 "
       pdb=" OA5 2YP A 501 "
    ideal  model  delta    sigma   weight residual
    1.421  1.225  0.196 2.00e-02 2.50e+03 9.63e+01
  bond pdb=" C5  2YP A 501 "
       pdb=" O5  2YP A 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.538 -0.126 2.00e-02 2.50e+03 3.94e+01
  bond pdb=" CAE 2YP A 501 "
       pdb=" NAD 2YP A 501 "
    ideal  model  delta    sigma   weight residual
    1.345  1.465 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CA1 2YP A 501 "
       pdb=" OA5 2YP A 501 "
    ideal  model  delta    sigma   weight residual
    1.400  1.285  0.115 2.00e-02 2.50e+03 3.30e+01
  bond pdb=" C2  2YP A 501 "
       pdb=" N2  2YP A 501 "
    ideal  model  delta    sigma   weight residual
    1.437  1.544 -0.107 2.00e-02 2.50e+03 2.86e+01
  ... (remaining 6127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.84: 11090
        8.84 -    17.67: 10
       17.67 -    26.51: 1
       26.51 -    35.34: 0
       35.34 -    44.18: 1
  Bond angle restraints: 11102
  Sorted by residual:
  angle pdb=" CA  VAL A 338 "
        pdb=" CB  VAL A 338 "
        pdb=" HB  VAL A 338 "
      ideal   model   delta    sigma   weight residual
     109.00   64.82   44.18 3.00e+00 1.11e-01 2.17e+02
  angle pdb=" N   THR A 191 "
        pdb=" CA  THR A 191 "
        pdb=" C   THR A 191 "
      ideal   model   delta    sigma   weight residual
     112.90  102.55   10.35 1.31e+00 5.83e-01 6.25e+01
  angle pdb=" N   PHE A 255 "
        pdb=" CA  PHE A 255 "
        pdb=" C   PHE A 255 "
      ideal   model   delta    sigma   weight residual
     111.07  102.94    8.13 1.07e+00 8.73e-01 5.77e+01
  angle pdb=" CA  LEU A 179 "
        pdb=" C   LEU A 179 "
        pdb=" O   LEU A 179 "
      ideal   model   delta    sigma   weight residual
     120.55  112.94    7.61 1.06e+00 8.90e-01 5.15e+01
  angle pdb=" N   GLU A 326 "
        pdb=" CA  GLU A 326 "
        pdb=" C   GLU A 326 "
      ideal   model   delta    sigma   weight residual
     111.14  104.03    7.11 1.08e+00 8.57e-01 4.34e+01
  ... (remaining 11097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.80: 2514
       19.80 -    39.59: 268
       39.59 -    59.39: 106
       59.39 -    79.19: 5
       79.19 -    98.99: 9
  Dihedral angle restraints: 2902
    sinusoidal: 1563
      harmonic: 1339
  Sorted by residual:
  dihedral pdb=" CA  ARG A 221 "
           pdb=" C   ARG A 221 "
           pdb=" N   ASN A 222 "
           pdb=" CA  ASN A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.05   19.95     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" C   ARG A 153 "
           pdb=" N   ARG A 153 "
           pdb=" CA  ARG A 153 "
           pdb=" CB  ARG A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.83   -9.77     0      2.50e+00 1.60e-01 1.53e+01
  dihedral pdb=" CA  ASN A 222 "
           pdb=" C   ASN A 222 "
           pdb=" N   ASN A 223 "
           pdb=" CA  ASN A 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.18  -17.82     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 2899 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 341
       0.057 -    0.114: 79
       0.114 -    0.171: 58
       0.171 -    0.228: 17
       0.228 -    0.285: 5
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CA  ARG A 153 "
            pdb=" N   ARG A 153 "
            pdb=" C   ARG A 153 "
            pdb=" CB  ARG A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA5 2YP A 501 "
            pdb=" CA4 2YP A 501 "
            pdb=" CA6 2YP A 501 "
            pdb=" OA5 2YP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67   -2.41   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE A 188 "
            pdb=" N   ILE A 188 "
            pdb=" C   ILE A 188 "
            pdb=" CB  ILE A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 497 not shown)

  Planarity restraints: 871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 124 "   -0.237 2.00e-02 2.50e+03   3.30e-01 1.63e+03
        pdb=" CD  GLN A 124 "    0.016 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 124 "    0.235 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 124 "   -0.006 2.00e-02 2.50e+03
        pdb="HE21 GLN A 124 "    0.515 2.00e-02 2.50e+03
        pdb="HE22 GLN A 124 "   -0.525 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 251 "    0.284 9.50e-02 1.11e+02   2.67e-01 1.41e+03
        pdb=" NE  ARG A 251 "    0.207 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 251 "    0.061 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 251 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 251 "   -0.047 2.00e-02 2.50e+03
        pdb="HH11 ARG A 251 "   -0.528 2.00e-02 2.50e+03
        pdb="HH12 ARG A 251 "    0.465 2.00e-02 2.50e+03
        pdb="HH21 ARG A 251 "   -0.126 2.00e-02 2.50e+03
        pdb="HH22 ARG A 251 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  79 "    0.228 9.50e-02 1.11e+02   2.43e-01 1.21e+03
        pdb=" NE  ARG A  79 "    0.133 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  79 "    0.028 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  79 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  79 "   -0.056 2.00e-02 2.50e+03
        pdb="HH11 ARG A  79 "    0.473 2.00e-02 2.50e+03
        pdb="HH12 ARG A  79 "   -0.451 2.00e-02 2.50e+03
        pdb="HH21 ARG A  79 "   -0.176 2.00e-02 2.50e+03
        pdb="HH22 ARG A  79 "    0.026 2.00e-02 2.50e+03
  ... (remaining 868 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 1054
        2.26 -     2.85: 13849
        2.85 -     3.43: 16040
        3.43 -     4.02: 20533
        4.02 -     4.60: 30793
  Nonbonded interactions: 82269
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 349 "
            pdb=" HG  SER A 350 "
     model   vdw
     1.679 2.450
  nonbonded pdb=" H   GLU A 140 "
            pdb=" HG3 GLU A 140 "
     model   vdw
     1.727 2.270
  nonbonded pdb=" HD1 PHE A 375 "
            pdb=" HB2 PHE A 384 "
     model   vdw
     1.731 2.270
  nonbonded pdb=" H   ILE A  49 "
            pdb="HG13 ILE A  49 "
     model   vdw
     1.734 2.270
  nonbonded pdb=" HA  VAL A 338 "
            pdb=" HB  VAL A 338 "
     model   vdw
     1.748 1.952
  ... (remaining 82264 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.470
  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:             0.110
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.320
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5982
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      :  0.012   0.196   3062  Z= 0.763
  Angle     :  1.575  11.761   4171  Z= 1.114
  Chirality :  0.075   0.285    500
  Planarity :  0.009   0.062    498
  Dihedral  : 17.440  98.986   1092
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 25.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 23.18 %
    Favored  : 75.83 %
  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: -3.17 (0.39), residues: 382
  helix: -2.03 (0.32), residues: 205
  sheet:  None (None), residues: 0
  loop : -2.09 (0.45), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A 307 
 HIS   0.004   0.002   HIS A 315 
 PHE   0.014   0.001   PHE A  52 
 TYR   0.009   0.001   TYR A  72 
 ARG   0.005   0.001   ARG A 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31897 (  139)
  hydrogen bonds       : angle      10.44046 (  396)
  covalent geometry    : bond        0.01185 ( 3062)
  covalent geometry    : angle       1.57453 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 VAL cc_start: 0.8404 (m) cc_final: 0.8196 (m)
REVERT: A  110 MET cc_start: 0.3780 (mtt) cc_final: 0.3332 (mtt)
REVERT: A  129 ASP cc_start: 0.6320 (t70) cc_final: 0.6086 (t0)
REVERT: A  231 ILE cc_start: 0.8765 (tp) cc_final: 0.8503 (mt)
REVERT: A  301 VAL cc_start: 0.8088 (m) cc_final: 0.7867 (t)
REVERT: A  407 GLU cc_start: 0.4972 (mt-10) cc_final: 0.4520 (pt0)
  outliers start: 3
  outliers final: 0
  residues processed: 96
  average time/residue: 0.3987
  time to fit residues: 46.3496
Evaluate side-chains
  71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.215595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.202952 restraints weight = 14406.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.207943 restraints weight = 6738.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.210693 restraints weight = 3523.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6273
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3062  Z= 0.179
  Angle     :  0.743   5.746   4171  Z= 0.382
  Chirality :  0.037   0.123    500
  Planarity :  0.005   0.046    498
  Dihedral  :  9.565  39.478    470
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.59 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.19 %
    Favored  : 75.50 %
  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: -2.77 (0.38), residues: 382
  helix: -1.42 (0.31), residues: 234
  sheet:  None (None), residues: 0
  loop : -2.39 (0.43), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 307 
 HIS   0.001   0.001   HIS A 315 
 PHE   0.013   0.002   PHE A 289 
 TYR   0.009   0.002   TYR A 367 
 ARG   0.004   0.001   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06628 (  139)
  hydrogen bonds       : angle       6.22629 (  396)
  covalent geometry    : bond        0.00371 ( 3062)
  covalent geometry    : angle       0.74277 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.7147 (ttt180) cc_final: 0.6737 (ttm110)
REVERT: A  110 MET cc_start: 0.4096 (mtt) cc_final: 0.3666 (mtt)
REVERT: A  129 ASP cc_start: 0.7345 (t70) cc_final: 0.6965 (t0)
REVERT: A  332 MET cc_start: 0.8504 (mtt) cc_final: 0.7914 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 79
  average time/residue: 0.3114
  time to fit residues: 30.0847
Evaluate side-chains
  70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue  312 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.208878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.195509 restraints weight = 14338.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.200785 restraints weight = 6791.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.203673 restraints weight = 3578.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6445
moved from start:          0.5009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3062  Z= 0.180
  Angle     :  0.681   5.516   4171  Z= 0.352
  Chirality :  0.037   0.130    500
  Planarity :  0.005   0.056    498
  Dihedral  :  8.909  45.707    470
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.90 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.19 %
    Favored  : 74.83 %
  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: -2.08 (0.40), residues: 382
  helix: -0.95 (0.32), residues: 238
  sheet:  None (None), residues: 0
  loop : -1.96 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 307 
 HIS   0.002   0.001   HIS A 315 
 PHE   0.014   0.002   PHE A  63 
 TYR   0.006   0.001   TYR A 234 
 ARG   0.003   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05662 (  139)
  hydrogen bonds       : angle       5.53772 (  396)
  covalent geometry    : bond        0.00374 ( 3062)
  covalent geometry    : angle       0.68053 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7450 (t60) cc_final: 0.7015 (t60)
REVERT: A  110 MET cc_start: 0.4184 (mtt) cc_final: 0.3753 (mtt)
REVERT: A  129 ASP cc_start: 0.7412 (t70) cc_final: 0.7059 (t0)
REVERT: A  332 MET cc_start: 0.8497 (mtt) cc_final: 0.7982 (mtt)
REVERT: A  379 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5394 (t-170)
  outliers start: 9
  outliers final: 5
  residues processed: 82
  average time/residue: 0.3072
  time to fit residues: 30.5078
Evaluate side-chains
  78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.208483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.195830 restraints weight = 14675.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.200930 restraints weight = 6879.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.203767 restraints weight = 3626.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6457
moved from start:          0.5517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3062  Z= 0.141
  Angle     :  0.616   5.316   4171  Z= 0.319
  Chirality :  0.035   0.133    500
  Planarity :  0.005   0.064    498
  Dihedral  :  8.331  50.752    470
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.85 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.52 %
    Favored  : 74.17 %
  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: -1.93 (0.41), residues: 382
  helix: -0.71 (0.33), residues: 239
  sheet:  None (None), residues: 0
  loop : -2.15 (0.46), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  83 
 HIS   0.001   0.001   HIS A 379 
 PHE   0.010   0.001   PHE A 255 
 TYR   0.006   0.001   TYR A 367 
 ARG   0.001   0.000   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04702 (  139)
  hydrogen bonds       : angle       5.18174 (  396)
  covalent geometry    : bond        0.00299 ( 3062)
  covalent geometry    : angle       0.61590 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7382 (t80)
REVERT: A  110 MET cc_start: 0.4206 (mtt) cc_final: 0.3772 (mtt)
REVERT: A  129 ASP cc_start: 0.7268 (t70) cc_final: 0.7026 (t0)
REVERT: A  332 MET cc_start: 0.8467 (mtt) cc_final: 0.7918 (mtt)
REVERT: A  379 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.5468 (t-170)
  outliers start: 10
  outliers final: 6
  residues processed: 77
  average time/residue: 0.3111
  time to fit residues: 29.1013
Evaluate side-chains
  78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0060
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.207469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.194828 restraints weight = 14652.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.200021 restraints weight = 6893.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.202845 restraints weight = 3590.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3062  Z= 0.134
  Angle     :  0.601   5.397   4171  Z= 0.311
  Chirality :  0.035   0.130    500
  Planarity :  0.005   0.068    498
  Dihedral  :  7.891  43.455    470
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.64 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.85 %
    Favored  : 74.50 %
  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: -1.57 (0.42), residues: 382
  helix: -0.43 (0.34), residues: 241
  sheet:  None (None), residues: 0
  loop : -2.01 (0.48), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 307 
 HIS   0.001   0.001   HIS A 315 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.004   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04258 (  139)
  hydrogen bonds       : angle       4.88603 (  396)
  covalent geometry    : bond        0.00290 ( 3062)
  covalent geometry    : angle       0.60116 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7552 (t60) cc_final: 0.7239 (t60)
REVERT: A  110 MET cc_start: 0.4066 (mtt) cc_final: 0.3645 (mtt)
REVERT: A  129 ASP cc_start: 0.7375 (t70) cc_final: 0.7166 (t0)
REVERT: A  332 MET cc_start: 0.8482 (mtt) cc_final: 0.7967 (mtt)
REVERT: A  379 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5470 (t-170)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.3011
  time to fit residues: 28.8008
Evaluate side-chains
  79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.206034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.193514 restraints weight = 14332.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.198660 restraints weight = 6770.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.201433 restraints weight = 3525.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.6196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3062  Z= 0.140
  Angle     :  0.613   6.367   4171  Z= 0.316
  Chirality :  0.036   0.137    500
  Planarity :  0.005   0.067    498
  Dihedral  :  7.789  47.451    470
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.69 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.18 %
    Favored  : 73.51 %
  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: -1.37 (0.43), residues: 382
  helix: -0.27 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.88 (0.49), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 307 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.011   0.001   PHE A 349 
 TYR   0.005   0.001   TYR A  72 
 ARG   0.003   0.000   ARG A 221 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  139)
  hydrogen bonds       : angle       4.80294 (  396)
  covalent geometry    : bond        0.00304 ( 3062)
  covalent geometry    : angle       0.61295 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7647 (t60) cc_final: 0.7291 (t60)
REVERT: A  110 MET cc_start: 0.4238 (mtt) cc_final: 0.3802 (mtt)
REVERT: A  129 ASP cc_start: 0.7457 (t0) cc_final: 0.7235 (t0)
REVERT: A  332 MET cc_start: 0.8456 (mtt) cc_final: 0.7926 (mtt)
REVERT: A  379 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5650 (t-170)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.2759
  time to fit residues: 27.4667
Evaluate side-chains
  81 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4395 r_free = 0.4395 target = 0.204577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.192701 restraints weight = 15051.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.197471 restraints weight = 7231.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.200025 restraints weight = 3843.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.6524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3062  Z= 0.140
  Angle     :  0.610   6.170   4171  Z= 0.316
  Chirality :  0.036   0.143    500
  Planarity :  0.005   0.068    498
  Dihedral  :  7.731  53.401    470
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.16 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.85 %
    Favored  : 73.51 %
  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: -1.23 (0.43), residues: 382
  helix: -0.12 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.90 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 307 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.014   0.001   PHE A 349 
 TYR   0.005   0.001   TYR A 152 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  139)
  hydrogen bonds       : angle       4.65718 (  396)
  covalent geometry    : bond        0.00308 ( 3062)
  covalent geometry    : angle       0.60999 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7695 (t60) cc_final: 0.7450 (t60)
REVERT: A  110 MET cc_start: 0.4181 (mtt) cc_final: 0.3727 (mtt)
REVERT: A  123 SER cc_start: 0.8301 (m) cc_final: 0.7607 (t)
REVERT: A  379 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.5918 (t-170)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.2756
  time to fit residues: 26.9527
Evaluate side-chains
  77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 22 optimal weight:    0.0010
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.4386

-------------------------------------------------------------------------------
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 = 0.4406 r_free = 0.4406 target = 0.205621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.193674 restraints weight = 14926.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.198405 restraints weight = 7294.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.201045 restraints weight = 3865.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.6739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3062  Z= 0.116
  Angle     :  0.590   6.999   4171  Z= 0.303
  Chirality :  0.035   0.146    500
  Planarity :  0.005   0.068    498
  Dihedral  :  7.599  54.665    470
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.90 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 22.52 %
    Favored  : 73.51 %
  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: -1.16 (0.43), residues: 382
  helix: -0.11 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.79 (0.50), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  83 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.010   0.001   PHE A 255 
 TYR   0.009   0.001   TYR A  72 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  139)
  hydrogen bonds       : angle       4.49143 (  396)
  covalent geometry    : bond        0.00261 ( 3062)
  covalent geometry    : angle       0.58969 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7556 (t60) cc_final: 0.7321 (t60)
REVERT: A   51 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: A  110 MET cc_start: 0.4113 (mtt) cc_final: 0.3668 (mtt)
REVERT: A  123 SER cc_start: 0.8245 (m) cc_final: 0.7582 (t)
REVERT: A  379 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.5820 (t-170)
  outliers start: 12
  outliers final: 10
  residues processed: 79
  average time/residue: 0.3670
  time to fit residues: 36.1955
Evaluate side-chains
  80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.2716

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.206838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.194915 restraints weight = 14814.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.199815 restraints weight = 7080.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.202442 restraints weight = 3710.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
moved from start:          0.6969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3062  Z= 0.112
  Angle     :  0.582   7.406   4171  Z= 0.298
  Chirality :  0.034   0.147    500
  Planarity :  0.005   0.068    498
  Dihedral  :  7.498  55.925    470
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.64 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.50 %
    Favored  : 72.52 %
  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: -1.06 (0.43), residues: 382
  helix: -0.04 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.70 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 307 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.011   0.001   PHE A 255 
 TYR   0.005   0.001   TYR A 152 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  139)
  hydrogen bonds       : angle       4.39162 (  396)
  covalent geometry    : bond        0.00254 ( 3062)
  covalent geometry    : angle       0.58219 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7607 (t60) cc_final: 0.7355 (t60)
REVERT: A   51 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7189 (t80)
REVERT: A  110 MET cc_start: 0.4207 (mtt) cc_final: 0.3792 (mtt)
REVERT: A  123 SER cc_start: 0.8173 (m) cc_final: 0.7528 (t)
REVERT: A  332 MET cc_start: 0.8153 (mtt) cc_final: 0.7210 (mtt)
REVERT: A  379 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5824 (t-170)
  outliers start: 9
  outliers final: 6
  residues processed: 79
  average time/residue: 0.3414
  time to fit residues: 32.8799
Evaluate side-chains
  77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.204363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.192404 restraints weight = 14781.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.197254 restraints weight = 6945.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.199900 restraints weight = 3641.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.7078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3062  Z= 0.133
  Angle     :  0.609   8.123   4171  Z= 0.311
  Chirality :  0.036   0.157    500
  Planarity :  0.005   0.064    498
  Dihedral  :  7.436  57.649    470
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.64 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 26.16 %
    Favored  : 71.52 %
  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: -0.99 (0.44), residues: 382
  helix: -0.01 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.65 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 307 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.013   0.001   PHE A 325 
 TYR   0.006   0.001   TYR A 152 
 ARG   0.004   0.000   ARG A 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  139)
  hydrogen bonds       : angle       4.42583 (  396)
  covalent geometry    : bond        0.00299 ( 3062)
  covalent geometry    : angle       0.60854 ( 4171)

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

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

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  764 Ramachandran restraints generated.
    382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 TRP cc_start: 0.7597 (t60) cc_final: 0.7375 (t60)
REVERT: A   51 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7184 (t80)
REVERT: A  110 MET cc_start: 0.4229 (mtt) cc_final: 0.3781 (mtt)
REVERT: A  123 SER cc_start: 0.8192 (m) cc_final: 0.7511 (t)
REVERT: A  332 MET cc_start: 0.8240 (mtt) cc_final: 0.7506 (mtt)
REVERT: A  379 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5991 (t-170)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.3100
  time to fit residues: 28.1900
Evaluate side-chains
  75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 SER
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   51 PHE
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  315 HIS
Chi-restraints excluded: chain A residue  379 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0870
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4376 r_free = 0.4376 target = 0.203526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.191863 restraints weight = 15151.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.196502 restraints weight = 7178.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.199112 restraints weight = 3787.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.7271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3062  Z= 0.126
  Angle     :  0.627  11.829   4171  Z= 0.314
  Chirality :  0.035   0.158    500
  Planarity :  0.005   0.064    498
  Dihedral  :  7.451  58.461    470
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.64 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 25.83 %
    Favored  : 71.19 %
  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: -0.96 (0.44), residues: 382
  helix:  0.03 (0.35), residues: 235
  sheet:  None (None), residues: 0
  loop : -1.65 (0.52), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 381 
 HIS   0.001   0.000   HIS A 315 
 PHE   0.014   0.001   PHE A 255 
 TYR   0.005   0.001   TYR A  72 
 ARG   0.003   0.000   ARG A 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  139)
  hydrogen bonds       : angle       4.37635 (  396)
  covalent geometry    : bond        0.00289 ( 3062)
  covalent geometry    : angle       0.62745 ( 4171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3175.08 seconds
wall clock time: 56 minutes 4.54 seconds (3364.54 seconds total)