Starting phenix.real_space_refine
on Wed Aug  5 03:32:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l5y_62848/08_2026/9l5y_62848.map"
  }
  resolution = 3.81
  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=  -0.000 sd=   0.013
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
     P      34      5.49       5
     S      12      5.16       5
     C    5039      2.51       5
     N    1443      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8123
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3691
          Classifications: {'peptide': 460}
          Link IDs: {'PTRANS': 19, 'TRANS': 440}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3702
          Classifications: {'peptide': 461}
          Link IDs: {'PTRANS': 19, 'TRANS': 441}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 386
          Classifications: {'RNA': 18}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 1, 'rna3p': 16}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 344
          Classifications: {'RNA': 16}
          Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 15}
          Chain breaks: 1
  Time building chain proxies: 1.34, per 1000 atoms: 0.16
  Number of scatterers: 8123
  At special positions: 0
  Unit cell: (175.497, 99.736, 68.089, 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      12     16.00
     P      34     15.00
     O    1595      8.00
     N    1443      7.00
     C    5039      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 273.4 milliseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1726

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 3 sheets defined
      67.9% alpha, 4.6% beta
      12 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.970A  pdb=" N   SER A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 41
    Processing helix  chain 'A' and resid 50 through 67
    Processing helix  chain 'A' and resid 67 through 81
    Processing helix  chain 'A' and resid 85 through 96
      removed outlier: 3.799A  pdb=" N   ALA A  89 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 104
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 137 through 151
    Processing helix  chain 'A' and resid 152 through 159
    Processing helix  chain 'A' and resid 167 through 176
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 198 through 211
      removed outlier: 3.542A  pdb=" N   MET A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 223
    Processing helix  chain 'A' and resid 225 through 233
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 5.034A  pdb=" N   ASN A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   ASN A 247 " --> pdb=" O   ARG A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 269
      removed outlier: 3.864A  pdb=" N   ARG A 269 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 276 through 291
      removed outlier: 3.555A  pdb=" N   TYR A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.506A  pdb=" N   SER A 306 " --> pdb=" O   GLU A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 355
    Processing helix  chain 'A' and resid 369 through 372
      removed outlier: 3.684A  pdb=" N   THR A 372 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 369 through 372'
    Processing helix  chain 'A' and resid 375 through 387
    Processing helix  chain 'A' and resid 392 through 401
      removed outlier: 3.610A  pdb=" N   ALA A 396 " --> pdb=" O   TYR A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 433
    Processing helix  chain 'A' and resid 466 through 475
    Processing helix  chain 'A' and resid 480 through 489
    Processing helix  chain 'B' and resid 26 through 35
    Processing helix  chain 'B' and resid 36 through 39
      removed outlier: 3.529A  pdb=" N   PHE B  39 " --> pdb=" O   SER B  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 36 through 39'
    Processing helix  chain 'B' and resid 50 through 67
    Processing helix  chain 'B' and resid 67 through 79
      removed outlier: 3.557A  pdb=" N   VAL B  71 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR B  77 " --> pdb=" O   SER B  73 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ARG B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 96
    Processing helix  chain 'B' and resid 99 through 104
    Processing helix  chain 'B' and resid 104 through 116
      removed outlier: 3.543A  pdb=" N   THR B 111 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 133
      removed outlier: 3.625A  pdb=" N   GLU B 124 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 150
      removed outlier: 3.617A  pdb=" N   ASP B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 167 through 176
      removed outlier: 3.508A  pdb=" N   HIS B 176 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 194
      removed outlier: 3.620A  pdb=" N   SER B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 197
      No H-bonds generated for 'chain 'B' and resid 195 through 197'
    Processing helix  chain 'B' and resid 198 through 209
    Processing helix  chain 'B' and resid 214 through 223
    Processing helix  chain 'B' and resid 225 through 236
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 238 through 251
      removed outlier: 5.192A  pdb=" N   ASN B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   ASN B 247 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   HIS B 251 " --> pdb=" O   ASN B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 255
    Processing helix  chain 'B' and resid 256 through 268
    Processing helix  chain 'B' and resid 276 through 290
      removed outlier: 3.532A  pdb=" N   TYR B 280 " --> pdb=" O   PHE B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 324 through 328
    Processing helix  chain 'B' and resid 338 through 355
      removed outlier: 3.560A  pdb=" N   ALA B 342 " --> pdb=" O   HIS B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 371
      No H-bonds generated for 'chain 'B' and resid 369 through 371'
    Processing helix  chain 'B' and resid 375 through 387
    Processing helix  chain 'B' and resid 392 through 401
      removed outlier: 3.586A  pdb=" N   ALA B 396 " --> pdb=" O   TYR B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 433
    Processing helix  chain 'B' and resid 466 through 477
      removed outlier: 4.063A  pdb=" N   VAL B 476 " --> pdb=" O   GLU B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 489
      removed outlier: 4.486A  pdb=" N   PHE B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367
      removed outlier: 6.710A  pdb=" N   THR A 317 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   TRP A 359 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   PHE A 319 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   PHE A 361 " --> pdb=" O   PHE A 319 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL A 321 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL A 411 " --> pdb=" O   HIS A 440 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   ILE A 442 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE A 413 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA A 439 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   ILE A 457 " --> pdb=" O   PRO A 453 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 365 through 367
      removed outlier: 6.660A  pdb=" N   THR B 317 " --> pdb=" O   GLU B 357 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   TRP B 359 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   PHE B 319 " --> pdb=" O   TRP B 359 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE B 361 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   VAL B 321 " --> pdb=" O   PHE B 361 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL B 411 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 414 through 415

    386 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      31 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2466
        1.34 -     1.45: 1383
        1.45 -     1.57: 4430
        1.57 -     1.69: 64
        1.69 -     1.81: 24
  Bond restraints: 8367
  Sorted by residual:
  bond pdb=" CG  GLN B 366 "
       pdb=" CD  GLN B 366 "
    ideal  model  delta    sigma   weight residual
    1.516  1.470  0.046 2.50e-02 1.60e+03 3.38e+00
  bond pdb=" CB  ARG A 184 "
       pdb=" CG  ARG A 184 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" CA  ILE B 413 "
       pdb=" CB  ILE B 413 "
    ideal  model  delta    sigma   weight residual
    1.531  1.543 -0.012 1.11e-02 8.12e+03 1.21e+00
  bond pdb=" N9    G D  11 "
       pdb=" C4    G D  11 "
    ideal  model  delta    sigma   weight residual
    1.375  1.384 -0.009 8.00e-03 1.56e+04 1.13e+00
  bond pdb=" C2    C F  10 "
       pdb=" N3    C F  10 "
    ideal  model  delta    sigma   weight residual
    1.353  1.361 -0.008 8.00e-03 1.56e+04 1.13e+00
  ... (remaining 8362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 11295
        2.62 -     5.25: 162
        5.25 -     7.87: 22
        7.87 -    10.49: 5
       10.49 -    13.12: 2
  Bond angle restraints: 11486
  Sorted by residual:
  angle pdb=" CA  MET B 327 "
        pdb=" CB  MET B 327 "
        pdb=" CG  MET B 327 "
      ideal   model   delta    sigma   weight residual
     114.10  123.57   -9.47 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" N   ALA B 362 "
        pdb=" CA  ALA B 362 "
        pdb=" C   ALA B 362 "
      ideal   model   delta    sigma   weight residual
     112.72  107.16    5.56 1.28e+00 6.10e-01 1.89e+01
  angle pdb=" CA  ARG B 105 "
        pdb=" CB  ARG B 105 "
        pdb=" CG  ARG B 105 "
      ideal   model   delta    sigma   weight residual
     114.10  121.85   -7.75 2.00e+00 2.50e-01 1.50e+01
  angle pdb=" CA  LEU B 187 "
        pdb=" CB  LEU B 187 "
        pdb=" CG  LEU B 187 "
      ideal   model   delta    sigma   weight residual
     116.30  129.42  -13.12 3.50e+00 8.16e-02 1.40e+01
  angle pdb=" O4'   A D  49 "
        pdb=" C1'   A D  49 "
        pdb=" N9    A D  49 "
      ideal   model   delta    sigma   weight residual
     108.20  111.03   -2.83 8.00e-01 1.56e+00 1.25e+01
  ... (remaining 11481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4235
       17.94 -    35.89: 577
       35.89 -    53.83: 173
       53.83 -    71.78: 65
       71.78 -    89.72: 27
  Dihedral angle restraints: 5077
    sinusoidal: 2403
      harmonic: 2674
  Sorted by residual:
  dihedral pdb=" CA  HIS A 338 "
           pdb=" C   HIS A 338 "
           pdb=" N   MET A 339 "
           pdb=" CA  MET A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  LEU B 304 "
           pdb=" C   LEU B 304 "
           pdb=" N   GLU B 305 "
           pdb=" CA  GLU B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.08   24.92     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  PHE B 361 "
           pdb=" C   PHE B 361 "
           pdb=" N   ALA B 362 "
           pdb=" CA  ALA B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.05   22.95     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 5074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 774
       0.031 -    0.062: 340
       0.062 -    0.093: 98
       0.093 -    0.123: 44
       0.123 -    0.154: 47
  Chirality restraints: 1303
  Sorted by residual:
  chirality pdb=" CG  LEU A  38 "
            pdb=" CB  LEU A  38 "
            pdb=" CD1 LEU A  38 "
            pdb=" CD2 LEU A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CA  PRO A 423 "
            pdb=" N   PRO A 423 "
            pdb=" C   PRO A 423 "
            pdb=" CB  PRO A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CG  LEU B 126 "
            pdb=" CB  LEU B 126 "
            pdb=" CD1 LEU B 126 "
            pdb=" CD2 LEU B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1300 not shown)

  Planarity restraints: 1333
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 366 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" CD  GLN B 366 "    0.038 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 366 "   -0.014 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 366 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 463 "    0.011 2.00e-02 2.50e+03   1.19e-02 3.53e+00
        pdb=" CG  TRP A 463 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 463 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 463 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 463 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 463 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 463 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 463 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 463 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 463 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  89 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.34e+00
        pdb=" C   ALA B  89 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ALA B  89 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA B  90 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1330 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 3378
        2.93 -     3.42: 8956
        3.42 -     3.92: 14649
        3.92 -     4.41: 16291
        4.41 -     4.90: 24517
  Nonbonded interactions: 67791
  Sorted by model distance:
  nonbonded pdb=" O   ASN B  99 "
            pdb=" OD1 ASN B  99 "
     model   vdw
     2.438 3.040
  nonbonded pdb=" O   SER B 405 "
            pdb=" OG  SER B 405 "
     model   vdw
     2.468 3.040
  nonbonded pdb=" N1    A F  12 "
            pdb=" O6    G F  51 "
     model   vdw
     2.502 2.496
  nonbonded pdb=" OD1 ASN B  99 "
            pdb=" OE2 GLU B 103 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" O   SER A 405 "
            pdb=" OG  SER A 405 "
     model   vdw
     2.556 3.040
  ... (remaining 67786 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 25 through 117 or resid 119 through 492))
}
ncs_group {
  reference = (chain 'D' and resid 8 through 55)
  selection = chain 'F'
}

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:             2.330
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.840
  Find NCS groups from input model:        0.100
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5130
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      :  0.003   0.046   8367  Z= 0.163
  Angle     :  0.799  13.119  11486  Z= 0.470
  Chirality :  0.046   0.154   1303
  Planarity :  0.005   0.056   1333
  Dihedral  : 19.336  89.721   3351
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 28.34 %
    Favored  : 68.11 %
  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: -0.80 (0.27), residues: 911
  helix:  0.03 (0.22), residues: 547
  sheet: -2.58 (0.61), residues: 62
  loop : -0.86 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 105 
 TYR   0.024   0.002   TYR B 128 
 PHE   0.020   0.002   PHE A  56 
 TRP   0.032   0.002   TRP A 463 
 HIS   0.012   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.16 ( 8367)
  covalent geometry    : angle       0.79884 /  0.47 (11486)
  hydrogen bonds       : bond        0.12874 /  8.84 (  417)
  hydrogen bonds       : angle       6.44303 /  4.51 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.6893 (mmm160) cc_final: 0.5426 (tpp-160)
REVERT: A  237 ASN cc_start: 0.7152 (t0) cc_final: 0.6817 (t0)
REVERT: B   77 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.2494 (p90)
REVERT: B   99 ASN cc_start: 0.8087 (t0) cc_final: 0.7772 (t0)
REVERT: B  105 ARG cc_start: 0.6959 (tpt90) cc_final: 0.6672 (tpt90)
REVERT: B  137 ARG cc_start: 0.7442 (mmp80) cc_final: 0.6163 (tpp80)
REVERT: B  209 MET cc_start: -0.0028 (OUTLIER) cc_final: -0.1101 (tpt)
REVERT: B  472 GLU cc_start: 0.5150 (tm-30) cc_final: 0.4695 (tt0)
  outliers start: 28
  outliers final: 22
  residues processed: 132
  average time/residue: 0.0777
  time to fit residues: 13.9151
Evaluate side-chains
  123 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 HIS
B  99 ASN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5208 r_free = 0.5208 target = 0.241061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.209804 restraints weight = 16262.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4927 r_free = 0.4927 target = 0.214659 restraints weight = 11352.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.217777 restraints weight = 8256.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4978 r_free = 0.4978 target = 0.219714 restraints weight = 6207.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.220498 restraints weight = 5995.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5180
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8367  Z= 0.160
  Angle     :  0.670  11.326  11486  Z= 0.338
  Chirality :  0.041   0.312   1303
  Planarity :  0.005   0.052   1333
  Dihedral  : 15.978  86.351   1596
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 22.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 23.38 %
    Favored  : 69.63 %
  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: -0.73 (0.28), residues: 911
  helix:  0.09 (0.22), residues: 558
  sheet: -2.89 (0.56), residues: 62
  loop : -0.78 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 104 
 TYR   0.024   0.002   TYR B 128 
 PHE   0.032   0.002   PHE A  39 
 TRP   0.013   0.002   TRP A 273 
 HIS   0.008   0.001   HIS B 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.16 ( 8367)
  covalent geometry    : angle       0.66984 /  0.34 (11486)
  hydrogen bonds       : bond        0.04731 /  3.29 (  417)
  hydrogen bonds       : angle       5.44341 /  3.87 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 101
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.7145 (mmm160) cc_final: 0.5778 (tpp-160)
REVERT: A  203 LYS cc_start: 0.7283 (ptmm) cc_final: 0.6910 (mmtm)
REVERT: A  237 ASN cc_start: 0.7133 (t0) cc_final: 0.6716 (m-40)
REVERT: A  424 TRP cc_start: 0.2322 (OUTLIER) cc_final: -0.0134 (m-90)
REVERT: B  203 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7294 (ptmm)
REVERT: B  209 MET cc_start: 0.0086 (OUTLIER) cc_final: -0.0531 (tpp)
REVERT: B  452 PHE cc_start: 0.6564 (t80) cc_final: 0.6333 (t80)
  outliers start: 55
  outliers final: 33
  residues processed: 140
  average time/residue: 0.0782
  time to fit residues: 14.8443
Evaluate side-chains
  122 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 87
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    0.0980
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0980
   chunk 4 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5215 r_free = 0.5215 target = 0.241785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.210736 restraints weight = 16145.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.215687 restraints weight = 11417.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.219383 restraints weight = 8203.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.220156 restraints weight = 6090.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.221852 restraints weight = 6021.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.4942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5121
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8367  Z= 0.131
  Angle     :  0.648  15.176  11486  Z= 0.321
  Chirality :  0.039   0.267   1303
  Planarity :  0.005   0.060   1333
  Dihedral  : 15.796  91.053   1587
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 23.63 %
    Favored  : 70.14 %
  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 (0.28), residues: 911
  helix:  0.06 (0.22), residues: 564
  sheet: -2.76 (0.56), residues: 64
  loop : -0.75 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 105 
 TYR   0.018   0.002   TYR B 280 
 PHE   0.031   0.002   PHE A  39 
 TRP   0.012   0.001   TRP A 273 
 HIS   0.008   0.001   HIS B 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 8367)
  covalent geometry    : angle       0.64759 /  0.32 (11486)
  hydrogen bonds       : bond        0.04454 /  3.06 (  417)
  hydrogen bonds       : angle       5.19431 /  3.71 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 98
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.6405 (mm) cc_final: 0.5947 (tt)
REVERT: A  137 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6998 (mmm-85)
REVERT: A  203 LYS cc_start: 0.7370 (ptmm) cc_final: 0.7065 (mmtm)
REVERT: A  237 ASN cc_start: 0.7241 (t0) cc_final: 0.6990 (t0)
REVERT: A  422 MET cc_start: 0.1800 (tpp) cc_final: 0.0818 (tmm)
REVERT: A  424 TRP cc_start: 0.2290 (OUTLIER) cc_final: -0.0302 (m-90)
REVERT: B   77 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.2423 (p90)
REVERT: B  104 ARG cc_start: 0.2630 (mtp180) cc_final: 0.2323 (mtp180)
REVERT: B  209 MET cc_start: 0.0121 (ppp) cc_final: -0.0476 (tpp)
  outliers start: 49
  outliers final: 37
  residues processed: 134
  average time/residue: 0.0700
  time to fit residues: 12.9424
Evaluate side-chains
  136 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  378 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0000
   chunk 82 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 189 GLN
A 251 HIS
B  87 ASN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5199 r_free = 0.5199 target = 0.240648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.208577 restraints weight = 16460.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.214171 restraints weight = 11346.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.217971 restraints weight = 8003.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.219453 restraints weight = 5915.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.220589 restraints weight = 5696.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5170
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8367  Z= 0.143
  Angle     :  0.647  12.550  11486  Z= 0.319
  Chirality :  0.042   0.464   1303
  Planarity :  0.004   0.058   1333
  Dihedral  : 15.694  95.166   1581
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 22.20
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.20 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 23.76 %
    Favored  : 69.63 %
  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: -0.75 (0.28), residues: 911
  helix:  0.06 (0.22), residues: 562
  sheet: -2.94 (0.56), residues: 62
  loop : -0.75 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 105 
 TYR   0.026   0.002   TYR B 377 
 PHE   0.032   0.002   PHE A  39 
 TRP   0.012   0.001   TRP A 463 
 HIS   0.007   0.001   HIS B 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 8367)
  covalent geometry    : angle       0.64679 /  0.32 (11486)
  hydrogen bonds       : bond        0.04241 /  2.92 (  417)
  hydrogen bonds       : angle       5.09835 /  3.65 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 98
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.6378 (mm) cc_final: 0.5903 (tt)
REVERT: A  203 LYS cc_start: 0.7352 (ptmm) cc_final: 0.7070 (mmtm)
REVERT: A  237 ASN cc_start: 0.7389 (t0) cc_final: 0.7092 (t0)
REVERT: A  288 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.3935 (tt0)
REVERT: A  358 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6700 (tm)
REVERT: A  366 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6949 (pm20)
REVERT: A  424 TRP cc_start: 0.2278 (OUTLIER) cc_final: -0.0241 (m-90)
REVERT: B   77 TYR cc_start: 0.5143 (OUTLIER) cc_final: 0.2601 (p90)
REVERT: B  209 MET cc_start: 0.0133 (OUTLIER) cc_final: -0.0483 (tpp)
  outliers start: 52
  outliers final: 36
  residues processed: 133
  average time/residue: 0.0850
  time to fit residues: 15.1333
Evaluate side-chains
  129 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 87
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 93 optimal weight:   30.0000
   chunk 11 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.238843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.208209 restraints weight = 16678.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.213179 restraints weight = 11102.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4942 r_free = 0.4942 target = 0.215830 restraints weight = 7699.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.219215 restraints weight = 5923.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4981 r_free = 0.4981 target = 0.219867 restraints weight = 5401.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5179
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8367  Z= 0.138
  Angle     :  0.646  14.344  11486  Z= 0.318
  Chirality :  0.041   0.373   1303
  Planarity :  0.004   0.068   1333
  Dihedral  : 15.634  89.495   1579
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.20 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 24.02 %
    Favored  : 69.38 %
  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: -0.68 (0.28), residues: 911
  helix:  0.07 (0.22), residues: 563
  sheet: -2.89 (0.56), residues: 64
  loop : -0.60 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 105 
 TYR   0.025   0.002   TYR B 377 
 PHE   0.032   0.002   PHE A  39 
 TRP   0.015   0.001   TRP A 463 
 HIS   0.008   0.001   HIS B 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 8367)
  covalent geometry    : angle       0.64562 /  0.32 (11486)
  hydrogen bonds       : bond        0.04070 /  2.82 (  417)
  hydrogen bonds       : angle       5.02494 /  3.60 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.6260 (mm) cc_final: 0.5684 (tt)
REVERT: A  128 TYR cc_start: 0.4503 (t80) cc_final: 0.4241 (t80)
REVERT: A  203 LYS cc_start: 0.7379 (ptmm) cc_final: 0.7125 (mmtm)
REVERT: A  237 ASN cc_start: 0.7385 (t0) cc_final: 0.6971 (t0)
REVERT: A  288 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.3914 (tt0)
REVERT: A  358 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6751 (tm)
REVERT: A  366 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7030 (pm20)
REVERT: A  422 MET cc_start: 0.2081 (tpp) cc_final: 0.1255 (tmm)
REVERT: A  424 TRP cc_start: 0.2302 (OUTLIER) cc_final: -0.0349 (m-90)
REVERT: B   77 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.2680 (p90)
REVERT: B  209 MET cc_start: 0.0233 (OUTLIER) cc_final: -0.0345 (tpp)
REVERT: B  305 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5914 (mp0)
REVERT: B  424 TRP cc_start: 0.3031 (OUTLIER) cc_final: 0.0677 (m-90)
  outliers start: 52
  outliers final: 35
  residues processed: 129
  average time/residue: 0.0875
  time to fit residues: 14.8678
Evaluate side-chains
  130 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 87
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  305 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 8 optimal weight:    0.5980
   chunk 88 optimal weight:    0.3980
   chunk 56 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 HIS
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5252 r_free = 0.5252 target = 0.243865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4952 r_free = 0.4952 target = 0.214492 restraints weight = 16444.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.218692 restraints weight = 11567.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5030 r_free = 0.5030 target = 0.221737 restraints weight = 8733.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.223962 restraints weight = 6990.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5071 r_free = 0.5071 target = 0.225731 restraints weight = 5827.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.5086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5179
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8367  Z= 0.123
  Angle     :  0.646  13.346  11486  Z= 0.318
  Chirality :  0.042   0.457   1303
  Planarity :  0.004   0.074   1333
  Dihedral  : 15.622  94.085   1578
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 20.32
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.20 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 26.05 %
    Favored  : 68.74 %
  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: -0.63 (0.28), residues: 911
  helix:  0.10 (0.21), residues: 562
  sheet: -2.83 (0.57), residues: 64
  loop : -0.58 (0.39), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 105 
 TYR   0.021   0.002   TYR B 377 
 PHE   0.032   0.002   PHE A  39 
 TRP   0.019   0.001   TRP A 463 
 HIS   0.012   0.001   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 8367)
  covalent geometry    : angle       0.64583 /  0.32 (11486)
  hydrogen bonds       : bond        0.03952 /  2.74 (  417)
  hydrogen bonds       : angle       4.96367 /  3.55 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.5779 (mm) cc_final: 0.5528 (tt)
REVERT: A  128 TYR cc_start: 0.4544 (t80) cc_final: 0.4255 (t80)
REVERT: A  237 ASN cc_start: 0.6905 (t0) cc_final: 0.6610 (t0)
REVERT: A  358 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6628 (tm)
REVERT: A  366 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7360 (pm20)
REVERT: A  422 MET cc_start: 0.2371 (tpp) cc_final: 0.1417 (tmm)
REVERT: A  424 TRP cc_start: 0.2580 (OUTLIER) cc_final: -0.0169 (m-90)
REVERT: B   77 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.2844 (p90)
REVERT: B  186 LEU cc_start: 0.8312 (mm) cc_final: 0.7807 (mm)
REVERT: B  209 MET cc_start: 0.0196 (OUTLIER) cc_final: -0.0318 (tpp)
REVERT: B  284 LEU cc_start: 0.6074 (tp) cc_final: 0.5864 (tt)
REVERT: B  305 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5703 (mp0)
REVERT: B  424 TRP cc_start: 0.3315 (OUTLIER) cc_final: 0.0986 (m-90)
  outliers start: 41
  outliers final: 31
  residues processed: 124
  average time/residue: 0.0919
  time to fit residues: 15.2152
Evaluate side-chains
  127 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 89
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  267 PHE
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  305 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    0.1980
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0670
   chunk 75 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.3436

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 HIS
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.245365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4964 r_free = 0.4964 target = 0.216258 restraints weight = 16093.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.220412 restraints weight = 11135.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.223508 restraints weight = 8340.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5064 r_free = 0.5064 target = 0.225833 restraints weight = 6600.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.5084 r_free = 0.5084 target = 0.227714 restraints weight = 5463.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.5096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5141
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8367  Z= 0.123
  Angle     :  0.655  13.455  11486  Z= 0.323
  Chirality :  0.041   0.356   1303
  Planarity :  0.004   0.078   1333
  Dihedral  : 15.556  95.073   1575
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 19.69
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.52 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 26.68 %
    Favored  : 67.47 %
  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: -0.58 (0.28), residues: 911
  helix:  0.15 (0.21), residues: 564
  sheet: -2.71 (0.57), residues: 64
  loop : -0.62 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 105 
 TYR   0.042   0.002   TYR B 377 
 PHE   0.033   0.002   PHE A  39 
 TRP   0.021   0.001   TRP A 463 
 HIS   0.012   0.001   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 8367)
  covalent geometry    : angle       0.65508 /  0.32 (11486)
  hydrogen bonds       : bond        0.03876 /  2.71 (  417)
  hydrogen bonds       : angle       4.89463 /  3.51 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 105
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 ASN cc_start: 0.6788 (t0) cc_final: 0.6480 (t0)
REVERT: A  358 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6633 (tm)
REVERT: A  366 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7338 (pm20)
REVERT: A  422 MET cc_start: 0.2248 (tpp) cc_final: 0.1464 (tmm)
REVERT: A  424 TRP cc_start: 0.2570 (OUTLIER) cc_final: -0.0141 (m-90)
REVERT: B   77 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.2737 (p90)
REVERT: B  186 LEU cc_start: 0.8274 (mm) cc_final: 0.7768 (mm)
REVERT: B  209 MET cc_start: 0.0219 (OUTLIER) cc_final: -0.0278 (tpp)
REVERT: B  424 TRP cc_start: 0.3306 (OUTLIER) cc_final: 0.0924 (m-90)
REVERT: B  472 GLU cc_start: 0.4735 (tm-30) cc_final: 0.4401 (tt0)
  outliers start: 46
  outliers final: 32
  residues processed: 135
  average time/residue: 0.0884
  time to fit residues: 16.1285
Evaluate side-chains
  133 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  122 HIS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 90 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 251 HIS
** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5245 r_free = 0.5245 target = 0.243001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.213598 restraints weight = 16682.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4989 r_free = 0.4989 target = 0.217567 restraints weight = 11812.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.220581 restraints weight = 9001.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.222629 restraints weight = 7231.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5053 r_free = 0.5053 target = 0.223972 restraints weight = 6100.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.5069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5205
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8367  Z= 0.138
  Angle     :  0.677  12.565  11486  Z= 0.333
  Chirality :  0.042   0.372   1303
  Planarity :  0.005   0.094   1333
  Dihedral  : 15.483  94.892   1571
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 20.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.41 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 28.08 %
    Favored  : 66.84 %
  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: -0.62 (0.28), residues: 911
  helix:  0.14 (0.21), residues: 566
  sheet: -2.75 (0.57), residues: 64
  loop : -0.67 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 105 
 TYR   0.040   0.002   TYR A 128 
 PHE   0.034   0.002   PHE A  39 
 TRP   0.021   0.001   TRP A 463 
 HIS   0.030   0.002   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 8367)
  covalent geometry    : angle       0.67740 /  0.33 (11486)
  hydrogen bonds       : bond        0.03852 /  2.68 (  417)
  hydrogen bonds       : angle       5.00065 /  3.57 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 97
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4016 (tt0)
REVERT: A  358 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6715 (tm)
REVERT: A  366 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7439 (pm20)
REVERT: A  422 MET cc_start: 0.2273 (tpp) cc_final: 0.1439 (tmm)
REVERT: A  424 TRP cc_start: 0.2602 (OUTLIER) cc_final: -0.0133 (m-90)
REVERT: B   77 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.2909 (p90)
REVERT: B   85 ARG cc_start: 0.5351 (mmm-85) cc_final: 0.4179 (ppt170)
REVERT: B  186 LEU cc_start: 0.8318 (mm) cc_final: 0.7870 (mm)
REVERT: B  209 MET cc_start: 0.0218 (OUTLIER) cc_final: -0.0278 (tpp)
REVERT: B  422 MET cc_start: 0.1620 (tpp) cc_final: 0.0842 (tmm)
REVERT: B  424 TRP cc_start: 0.3336 (OUTLIER) cc_final: 0.1370 (m-90)
  outliers start: 40
  outliers final: 32
  residues processed: 123
  average time/residue: 0.0915
  time to fit residues: 14.9896
Evaluate side-chains
  129 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 90
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   77 TYR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0870
   chunk 85 optimal weight:    7.9990
   chunk 77 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 HIS
A 251 HIS
** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.242941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4973 r_free = 0.4973 target = 0.215127 restraints weight = 16695.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.217739 restraints weight = 12455.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.221252 restraints weight = 9074.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.222308 restraints weight = 7250.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.222945 restraints weight = 6478.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.5055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5231
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8367  Z= 0.135
  Angle     :  0.687  14.902  11486  Z= 0.338
  Chirality :  0.042   0.368   1303
  Planarity :  0.005   0.097   1333
  Dihedral  : 15.504  93.508   1571
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.41 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 27.70 %
    Favored  : 67.22 %
  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: -0.61 (0.28), residues: 911
  helix:  0.15 (0.22), residues: 560
  sheet: -2.79 (0.57), residues: 64
  loop : -0.66 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG B 105 
 TYR   0.035   0.002   TYR B 377 
 PHE   0.035   0.002   PHE A  39 
 TRP   0.026   0.001   TRP A 463 
 HIS   0.007   0.001   HIS A 122 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8367)
  covalent geometry    : angle       0.68704 /  0.34 (11486)
  hydrogen bonds       : bond        0.03911 /  2.73 (  417)
  hydrogen bonds       : angle       4.96795 /  3.56 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 94
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 LYS cc_start: 0.6817 (mmtm) cc_final: 0.5857 (mmmt)
REVERT: A  288 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.4024 (tt0)
REVERT: A  358 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6734 (tm)
REVERT: A  366 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7410 (pm20)
REVERT: A  422 MET cc_start: 0.2231 (tpp) cc_final: 0.1483 (tmm)
REVERT: A  424 TRP cc_start: 0.2527 (OUTLIER) cc_final: -0.0193 (m-90)
REVERT: B  186 LEU cc_start: 0.8234 (mm) cc_final: 0.7808 (mm)
REVERT: B  209 MET cc_start: 0.0271 (OUTLIER) cc_final: -0.0264 (tpp)
REVERT: B  424 TRP cc_start: 0.3279 (OUTLIER) cc_final: 0.1684 (m-90)
REVERT: B  472 GLU cc_start: 0.4550 (tm-30) cc_final: 0.4172 (tt0)
  outliers start: 40
  outliers final: 31
  residues processed: 120
  average time/residue: 0.0838
  time to fit residues: 13.4453
Evaluate side-chains
  121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 84
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 92 optimal weight:   30.0000
   chunk 72 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 HIS
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5218 r_free = 0.5218 target = 0.236344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.201867 restraints weight = 15366.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4925 r_free = 0.4925 target = 0.207009 restraints weight = 10216.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.210822 restraints weight = 7449.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4995 r_free = 0.4995 target = 0.213693 restraints weight = 5816.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5011 r_free = 0.5011 target = 0.215526 restraints weight = 4747.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.5056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5223
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8367  Z= 0.136
  Angle     :  0.702  14.282  11486  Z= 0.349
  Chirality :  0.042   0.370   1303
  Planarity :  0.005   0.124   1333
  Dihedral  : 15.434  91.898   1569
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.52 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 27.83 %
    Favored  : 66.71 %
  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: -0.57 (0.28), residues: 911
  helix:  0.18 (0.22), residues: 557
  sheet: -2.83 (0.56), residues: 64
  loop : -0.62 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.000   ARG B 105 
 TYR   0.024   0.002   TYR A 128 
 PHE   0.035   0.002   PHE A  39 
 TRP   0.032   0.002   TRP A 463 
 HIS   0.014   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 8367)
  covalent geometry    : angle       0.70185 /  0.35 (11486)
  hydrogen bonds       : bond        0.03906 /  2.73 (  417)
  hydrogen bonds       : angle       4.95195 /  3.55 ( 1186)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 LYS cc_start: 0.6983 (mmtm) cc_final: 0.5969 (mmmt)
REVERT: A  288 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.3995 (tt0)
REVERT: A  358 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6738 (tm)
REVERT: A  366 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7447 (pm20)
REVERT: A  422 MET cc_start: 0.2235 (tpp) cc_final: 0.1454 (tmm)
REVERT: A  424 TRP cc_start: 0.2499 (OUTLIER) cc_final: -0.0259 (m-90)
REVERT: B  103 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6340 (pm20)
REVERT: B  186 LEU cc_start: 0.8375 (mm) cc_final: 0.7810 (mm)
REVERT: B  209 MET cc_start: 0.0100 (OUTLIER) cc_final: -0.0378 (tpp)
REVERT: B  422 MET cc_start: 0.1035 (tpp) cc_final: 0.0436 (tmm)
REVERT: B  424 TRP cc_start: 0.3395 (OUTLIER) cc_final: 0.1616 (m-90)
REVERT: B  472 GLU cc_start: 0.4659 (tm-30) cc_final: 0.4236 (tt0)
  outliers start: 43
  outliers final: 30
  residues processed: 121
  average time/residue: 0.0927
  time to fit residues: 15.0471
Evaluate side-chains
  125 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 88
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  424 TRP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  103 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  361 PHE
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  424 TRP
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  444 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 122 HIS
A 251 HIS
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5217 r_free = 0.5217 target = 0.239601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.211093 restraints weight = 16795.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.215607 restraints weight = 12035.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.217069 restraints weight = 9246.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.219269 restraints weight = 7275.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.219318 restraints weight = 6260.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.5020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5325
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8367  Z= 0.164
  Angle     :  0.732  13.824  11486  Z= 0.361
  Chirality :  0.044   0.385   1303
  Planarity :  0.005   0.095   1333
  Dihedral  : 15.434  87.384   1569
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 23.27
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.52 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 28.84 %
    Favored  : 66.58 %
  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: -0.78 (0.28), residues: 911
  helix:  0.03 (0.21), residues: 558
  sheet: -3.22 (0.55), residues: 62
  loop : -0.66 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG B 105 
 TYR   0.025   0.002   TYR A 128 
 PHE   0.036   0.003   PHE A  39 
 TRP   0.026   0.002   TRP A 463 
 HIS   0.016   0.002   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.16 ( 8367)
  covalent geometry    : angle       0.73216 /  0.36 (11486)
  hydrogen bonds       : bond        0.03949 /  2.74 (  417)
  hydrogen bonds       : angle       5.04053 /  3.61 ( 1186)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1222.41 seconds
wall clock time: 21 minutes 52.59 seconds (1312.59 seconds total)