Starting phenix.real_space_refine
on Fri Aug 22 19:28:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlp_36403/08_2025/8jlp_36403.map"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    4687      2.51       5
     N    1267      2.21       5
     O    1331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7343
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1972
          Classifications: {'peptide': 240}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2310
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'UJU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.24
  Number of scatterers: 7343
  At special positions: 0
  Unit cell: (102.85, 132.6, 80.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1331      8.00
     N    1267      7.00
     C    4687      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03

  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: 0.59
  Conformation dependent library (CDL) restraints added in 477.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1746

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      46.6% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.585A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 4.023A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.849A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 4.465A  pdb=" N   LEU A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.710A  pdb=" N   TYR A 311 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 349
      removed outlier: 4.347A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 387
      removed outlier: 4.175A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 30 through 37
    Processing helix  chain 'R' and resid 20 through 50
      removed outlier: 3.673A  pdb=" N   HIS R  50 " --> pdb=" O   VAL R  46 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 87
      removed outlier: 3.632A  pdb=" N   SER R  80 " --> pdb=" O   VAL R  76 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG R  83 " --> pdb=" O   TYR R  79 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER R  84 " --> pdb=" O   SER R  80 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA R  85 " --> pdb=" O   MET R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 3.552A  pdb=" N   ILE R  98 " --> pdb=" O   VAL R  94 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ILE R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   MET R 105 " --> pdb=" O   SER R 101 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASP R 127 " --> pdb=" O   TYR R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 131
      removed outlier: 3.920A  pdb=" N   TYR R 131 " --> pdb=" O   PRO R 128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 128 through 131'
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
      removed outlier: 3.565A  pdb=" N   PHE R 154 " --> pdb=" O   VAL R 150 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE R 159 " --> pdb=" O   ALA R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 200 through 228
    Processing helix  chain 'R' and resid 247 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 275 through 278
      removed outlier: 3.847A  pdb=" N   HIS R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 275 through 278'
    Processing helix  chain 'R' and resid 282 through 304
      removed outlier: 3.848A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
      removed outlier: 3.659A  pdb=" N   TYR R 304 " --> pdb=" O   ASN R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 319
      removed outlier: 3.507A  pdb=" N   ARG R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 7 through 24
    Processing helix  chain 'Y' and resid 29 through 45
      removed outlier: 3.502A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45
      removed outlier: 3.721A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245
      removed outlier: 6.522A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.617A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.790A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.617A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.748A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 152 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191
      removed outlier: 7.100A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.092A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 277
      removed outlier: 3.924A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 293 through 294

    363 hydrogen bonds defined for protein.
    1059 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.82 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: 2373
        1.34 -     1.46: 1768
        1.46 -     1.58: 3278
        1.58 -     1.70: 0
        1.70 -     1.82: 86
  Bond restraints: 7505
  Sorted by residual:
  bond pdb=" N1  UJU R 401 "
       pdb=" N2  UJU R 401 "
    ideal  model  delta    sigma   weight residual
    1.316  1.351 -0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" C16 UJU R 401 "
       pdb=" C4  UJU R 401 "
    ideal  model  delta    sigma   weight residual
    1.416  1.383  0.033 2.00e-02 2.50e+03 2.76e+00
  bond pdb=" C12 UJU R 401 "
       pdb=" C13 UJU R 401 "
    ideal  model  delta    sigma   weight residual
    1.536  1.507  0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C10 UJU R 401 "
       pdb=" C11 UJU R 401 "
    ideal  model  delta    sigma   weight residual
    1.547  1.518  0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" CG  GLU A 344 "
       pdb=" CD  GLU A 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 2.50e-02 1.60e+03 2.00e+00
  ... (remaining 7500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 9960
        1.91 -     3.83: 162
        3.83 -     5.74: 25
        5.74 -     7.66: 9
        7.66 -     9.57: 1
  Bond angle restraints: 10157
  Sorted by residual:
  angle pdb=" N   GLU A 344 "
        pdb=" CA  GLU A 344 "
        pdb=" CB  GLU A 344 "
      ideal   model   delta    sigma   weight residual
     110.28  116.05   -5.77 1.55e+00 4.16e-01 1.39e+01
  angle pdb=" CA  GLU A 344 "
        pdb=" CB  GLU A 344 "
        pdb=" CG  GLU A 344 "
      ideal   model   delta    sigma   weight residual
     114.10  120.48   -6.38 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" C   ILE B  81 "
        pdb=" N   TRP B  82 "
        pdb=" CA  TRP B  82 "
      ideal   model   delta    sigma   weight residual
     122.64  127.90   -5.26 1.70e+00 3.46e-01 9.56e+00
  angle pdb=" N   VAL B  90 "
        pdb=" CA  VAL B  90 "
        pdb=" C   VAL B  90 "
      ideal   model   delta    sigma   weight residual
     112.96  109.96    3.00 1.00e+00 1.00e+00 8.98e+00
  angle pdb=" C   ASP Y  48 "
        pdb=" CA  ASP Y  48 "
        pdb=" CB  ASP Y  48 "
      ideal   model   delta    sigma   weight residual
     111.20  109.14    2.06 7.10e-01 1.98e+00 8.42e+00
  ... (remaining 10152 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3997
       17.86 -    35.71: 374
       35.71 -    53.57: 78
       53.57 -    71.42: 14
       71.42 -    89.28: 9
  Dihedral angle restraints: 4472
    sinusoidal: 1778
      harmonic: 2694
  Sorted by residual:
  dihedral pdb=" CB  GLU A 370 "
           pdb=" CG  GLU A 370 "
           pdb=" CD  GLU A 370 "
           pdb=" OE1 GLU A 370 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.28   89.28     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  ARG A 228 "
           pdb=" C   ARG A 228 "
           pdb=" N   ASP A 229 "
           pdb=" CA  ASP A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.88  -16.12     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  ASP A 368 "
           pdb=" CB  ASP A 368 "
           pdb=" CG  ASP A 368 "
           pdb=" OD1 ASP A 368 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.36   53.36     1      2.00e+01 2.50e-03 9.68e+00
  ... (remaining 4469 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 694
       0.032 -    0.063: 299
       0.063 -    0.095: 95
       0.095 -    0.127: 44
       0.127 -    0.158: 4
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  GLU A 344 "
            pdb=" N   GLU A 344 "
            pdb=" C   GLU A 344 "
            pdb=" CB  GLU A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  VAL B 307 "
            pdb=" N   VAL B 307 "
            pdb=" C   VAL B 307 "
            pdb=" CB  VAL B 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1284
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C4  UJU R 401 "    0.060 2.00e-02 2.50e+03   6.75e-02 5.70e+01
        pdb=" C5  UJU R 401 "   -0.025 2.00e-02 2.50e+03
        pdb=" C6  UJU R 401 "    0.081 2.00e-02 2.50e+03
        pdb=" N3  UJU R 401 "   -0.109 2.00e-02 2.50e+03
        pdb=" O1  UJU R 401 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 254 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" C   GLY R 254 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY R 254 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ILE R 255 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 380 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   ARG A 380 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 380 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASP A 381 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1281 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 819
        2.75 -     3.29: 7379
        3.29 -     3.82: 11904
        3.82 -     4.36: 13635
        4.36 -     4.90: 23697
  Nonbonded interactions: 57434
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP R 264 "
            pdb=" OD1 ASN R 296 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   ARG A 333 "
            pdb=" NH1 ARG A 333 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   CYS B 103 "
            pdb=" NH1 ARG B 150 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" ND2 ASN B 119 "
            pdb=" O   THR B 143 "
     model   vdw
     2.307 3.120
  ... (remaining 57429 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
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   0.036   7506  Z= 0.158
  Angle     :  0.635   9.570  10159  Z= 0.341
  Chirality :  0.042   0.158   1136
  Planarity :  0.004   0.068   1284
  Dihedral  : 14.931  89.276   2723
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.28), residues: 909
  helix:  1.41 (0.27), residues: 383
  sheet: -0.75 (0.44), residues: 139
  loop : -1.68 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 283 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.013   0.002   PHE R 165 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7505)
  covalent geometry    : angle       0.63460 (10157)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.82888 (    2)
  hydrogen bonds       : bond        0.13173 (  363)
  hydrogen bonds       : angle       6.17907 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.205 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0934
  time to fit residues: 14.9612
Evaluate side-chains
  91 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 225 HIS
** B 340 ASN ** 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 = 0.4833 r_free = 0.4833 target = 0.252794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.205279 restraints weight = 8011.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4444 rms_B_bonded: 3.15
r_work: 0.4124 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.0966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7506  Z= 0.127
  Angle     :  0.571   7.589  10159  Z= 0.300
  Chirality :  0.041   0.143   1136
  Planarity :  0.004   0.050   1284
  Dihedral  :  6.672  81.843   1021
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.31 %
    Favored  : 89.18 %
  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 aren not related in a simple way.
  whole: -0.03 (0.29), residues: 909
  helix:  1.64 (0.27), residues: 394
  sheet: -0.83 (0.42), residues: 154
  loop : -1.54 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  22 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.021   0.001   PHE R 154 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7505)
  covalent geometry    : angle       0.57130 (10157)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       1.02365 (    2)
  hydrogen bonds       : bond        0.05056 (  363)
  hydrogen bonds       : angle       4.84331 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.7760 (pttm) cc_final: 0.7439 (ptpt)
REVERT: A  344 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7582 (pm20)
REVERT: B  225 HIS cc_start: 0.5172 (OUTLIER) cc_final: 0.4466 (m-70)
REVERT: R  178 CYS cc_start: 0.8302 (m) cc_final: 0.8093 (m)
REVERT: R  196 MET cc_start: 0.7550 (mmt) cc_final: 0.7291 (mmm)
  outliers start: 12
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0858
  time to fit residues: 12.3169
Evaluate side-chains
  105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 17 optimal weight:   20.0000
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.251546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.190217 restraints weight = 8091.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 3.00
r_work: 0.4146 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7506  Z= 0.133
  Angle     :  0.555   7.600  10159  Z= 0.292
  Chirality :  0.042   0.144   1136
  Planarity :  0.004   0.049   1284
  Dihedral  :  6.404  79.989   1021
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.70 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.29), residues: 909
  helix:  1.74 (0.27), residues: 395
  sheet: -0.67 (0.42), residues: 156
  loop : -1.45 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  20 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.021   0.001   PHE R 154 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7505)
  covalent geometry    : angle       0.55467 (10157)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.85409 (    2)
  hydrogen bonds       : bond        0.04977 (  363)
  hydrogen bonds       : angle       4.70621 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7350 (mpp) cc_final: 0.6700 (mpp)
REVERT: A  278 ASN cc_start: 0.7377 (m-40) cc_final: 0.7090 (m-40)
REVERT: A  289 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7774 (tt)
REVERT: R  178 CYS cc_start: 0.8337 (m) cc_final: 0.8134 (m)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0839
  time to fit residues: 12.3975
Evaluate side-chains
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 87 optimal weight:   30.0000
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:   20.0000
   chunk 53 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.253783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.193482 restraints weight = 8216.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.95
r_work: 0.4173 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7506  Z= 0.111
  Angle     :  0.523   8.288  10159  Z= 0.274
  Chirality :  0.041   0.144   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.056  76.302   1021
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.21 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.29), residues: 909
  helix:  1.89 (0.27), residues: 394
  sheet: -0.60 (0.42), residues: 157
  loop : -1.37 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R 154 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7505)
  covalent geometry    : angle       0.52321 (10157)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.67245 (    2)
  hydrogen bonds       : bond        0.04381 (  363)
  hydrogen bonds       : angle       4.52365 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7360 (mpp) cc_final: 0.6787 (mpp)
REVERT: A  211 LYS cc_start: 0.7720 (pttm) cc_final: 0.7366 (ptpt)
REVERT: A  278 ASN cc_start: 0.7364 (m-40) cc_final: 0.7046 (m-40)
REVERT: B  134 ARG cc_start: 0.8234 (ptp-110) cc_final: 0.7804 (ptp-110)
REVERT: R  196 MET cc_start: 0.7592 (mmt) cc_final: 0.7331 (mmm)
  outliers start: 14
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0776
  time to fit residues: 11.3096
Evaluate side-chains
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0170
   chunk 56 optimal weight:    7.9990
   chunk 20 optimal weight:    0.5980
   chunk 50 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 225 HIS
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.254259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.193327 restraints weight = 8135.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 3.01
r_work: 0.4174 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7506  Z= 0.107
  Angle     :  0.521   7.249  10159  Z= 0.272
  Chirality :  0.041   0.229   1136
  Planarity :  0.003   0.047   1284
  Dihedral  :  5.811  72.365   1021
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.59 %
    Favored  : 82.64 %
  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 aren not related in a simple way.
  whole:  0.39 (0.29), residues: 909
  helix:  2.03 (0.27), residues: 388
  sheet: -0.59 (0.42), residues: 159
  loop : -1.34 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  20 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R 154 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7505)
  covalent geometry    : angle       0.52108 (10157)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.60681 (    2)
  hydrogen bonds       : bond        0.04172 (  363)
  hydrogen bonds       : angle       4.41751 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7443 (mpp) cc_final: 0.6932 (mpp)
REVERT: A  211 LYS cc_start: 0.7769 (pttm) cc_final: 0.7372 (ptpt)
REVERT: A  278 ASN cc_start: 0.7292 (m-40) cc_final: 0.6950 (m-40)
REVERT: B  134 ARG cc_start: 0.8178 (ptp-110) cc_final: 0.7715 (ptp-110)
REVERT: R  196 MET cc_start: 0.7549 (mmt) cc_final: 0.7277 (mmm)
  outliers start: 22
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0749
  time to fit residues: 11.2100
Evaluate side-chains
  106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  123 TYR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0970
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B  36 ASN
B 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.249252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.201616 restraints weight = 8180.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.4416 rms_B_bonded: 3.37
r_work: 0.4091 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7506  Z= 0.148
  Angle     :  0.567   8.391  10159  Z= 0.297
  Chirality :  0.043   0.155   1136
  Planarity :  0.004   0.047   1284
  Dihedral  :  6.218  78.003   1021
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.35 %
    Favored  : 81.89 %
  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 aren not related in a simple way.
  whole:  0.26 (0.29), residues: 909
  helix:  1.87 (0.27), residues: 390
  sheet: -0.66 (0.42), residues: 156
  loop : -1.36 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 342 
 TYR   0.016   0.001   TYR A  37 
 PHE   0.017   0.002   PHE A 290 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7505)
  covalent geometry    : angle       0.56686 (10157)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.90214 (    2)
  hydrogen bonds       : bond        0.05040 (  363)
  hydrogen bonds       : angle       4.56752 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7483 (mpp) cc_final: 0.6961 (mpp)
REVERT: A  221 MET cc_start: 0.7067 (mmt) cc_final: 0.6858 (mmt)
REVERT: A  244 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7807 (mt)
REVERT: A  278 ASN cc_start: 0.7456 (m-40) cc_final: 0.7129 (m-40)
REVERT: A  289 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7846 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0697
  time to fit residues: 11.4731
Evaluate side-chains
  109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 16 optimal weight:    0.1980
   chunk 55 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0670
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 225 HIS
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.252778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.191488 restraints weight = 8188.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.4313 rms_B_bonded: 3.03
r_work: 0.4151 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7506  Z= 0.110
  Angle     :  0.528   8.262  10159  Z= 0.277
  Chirality :  0.041   0.143   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.019  74.414   1021
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.86 %
    Favored  : 80.38 %
  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 aren not related in a simple way.
  whole:  0.35 (0.29), residues: 909
  helix:  2.01 (0.27), residues: 387
  sheet: -0.63 (0.42), residues: 156
  loop : -1.36 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 134 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 290 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7505)
  covalent geometry    : angle       0.52785 (10157)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.63376 (    2)
  hydrogen bonds       : bond        0.04333 (  363)
  hydrogen bonds       : angle       4.42030 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7144 (tpp-160) cc_final: 0.6647 (mmm160)
REVERT: A   60 MET cc_start: 0.7501 (mpp) cc_final: 0.7032 (mpp)
REVERT: A  211 LYS cc_start: 0.7729 (pttm) cc_final: 0.7362 (ptpt)
REVERT: A  244 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7761 (mp)
REVERT: A  278 ASN cc_start: 0.7352 (m-40) cc_final: 0.6988 (m-40)
REVERT: A  279 ASN cc_start: 0.5555 (t0) cc_final: 0.5305 (t0)
REVERT: A  289 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: B  134 ARG cc_start: 0.8242 (ptp-110) cc_final: 0.7584 (ptm160)
REVERT: B  225 HIS cc_start: 0.5123 (OUTLIER) cc_final: 0.4531 (m-70)
REVERT: R  196 MET cc_start: 0.7574 (mmt) cc_final: 0.7297 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0817
  time to fit residues: 12.7602
Evaluate side-chains
  111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue   51 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  123 TYR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.251526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.203211 restraints weight = 8269.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.4424 rms_B_bonded: 3.04
r_work: 0.4136 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7506  Z= 0.123
  Angle     :  0.538   7.588  10159  Z= 0.282
  Chirality :  0.041   0.145   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.040  74.520   1021
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.98 %
    Favored  : 80.13 %
  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 aren not related in a simple way.
  whole:  0.32 (0.29), residues: 909
  helix:  1.97 (0.27), residues: 387
  sheet: -0.60 (0.42), residues: 156
  loop : -1.37 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.011   0.001   TYR A  37 
 PHE   0.013   0.001   PHE A 290 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.011   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7505)
  covalent geometry    : angle       0.53759 (10157)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.70577 (    2)
  hydrogen bonds       : bond        0.04474 (  363)
  hydrogen bonds       : angle       4.43256 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7236 (tpp-160) cc_final: 0.6731 (mmm160)
REVERT: A   60 MET cc_start: 0.7522 (mpp) cc_final: 0.7052 (mpp)
REVERT: A  211 LYS cc_start: 0.7745 (pttm) cc_final: 0.7389 (ptpt)
REVERT: A  221 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6607 (mmp)
REVERT: A  244 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (mt)
REVERT: A  278 ASN cc_start: 0.7458 (m-40) cc_final: 0.7096 (m-40)
REVERT: A  279 ASN cc_start: 0.5700 (t0) cc_final: 0.5457 (t0)
REVERT: B  134 ARG cc_start: 0.8278 (ptp-110) cc_final: 0.7710 (ptm160)
REVERT: B  225 HIS cc_start: 0.5180 (OUTLIER) cc_final: 0.4479 (m-70)
REVERT: R  196 MET cc_start: 0.7644 (mmt) cc_final: 0.7368 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0670
  time to fit residues: 10.5251
Evaluate side-chains
  115 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue   51 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0020
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.253197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.205394 restraints weight = 8043.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.4440 rms_B_bonded: 2.95
r_work: 0.4162 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7506  Z= 0.113
  Angle     :  0.558  12.692  10159  Z= 0.287
  Chirality :  0.042   0.265   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  5.955  72.092   1021
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.23 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.29), residues: 909
  helix:  2.00 (0.27), residues: 387
  sheet: -0.48 (0.42), residues: 150
  loop : -1.43 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.001   PHE A 290 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7505)
  covalent geometry    : angle       0.55798 (10157)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.60679 (    2)
  hydrogen bonds       : bond        0.04230 (  363)
  hydrogen bonds       : angle       4.41064 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7067 (mpp)
REVERT: A  211 LYS cc_start: 0.7743 (pttm) cc_final: 0.7369 (ptpt)
REVERT: A  244 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7737 (mp)
REVERT: A  278 ASN cc_start: 0.7375 (m-40) cc_final: 0.7004 (m-40)
REVERT: A  279 ASN cc_start: 0.5632 (t0) cc_final: 0.5348 (t0)
REVERT: B  134 ARG cc_start: 0.8232 (ptp-110) cc_final: 0.7647 (ptm160)
REVERT: R  196 MET cc_start: 0.7599 (mmt) cc_final: 0.7323 (mmm)
  outliers start: 23
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0680
  time to fit residues: 10.9982
Evaluate side-chains
  114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue   51 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0020
   chunk 86 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.255455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.195145 restraints weight = 8250.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4350 rms_B_bonded: 2.98
r_work: 0.4191 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7506  Z= 0.108
  Angle     :  0.545  11.974  10159  Z= 0.279
  Chirality :  0.041   0.145   1136
  Planarity :  0.003   0.049   1284
  Dihedral  :  5.660  65.021   1021
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.49 %
    Favored  : 78.99 %
  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 aren not related in a simple way.
  whole:  0.42 (0.29), residues: 909
  helix:  2.07 (0.27), residues: 388
  sheet: -0.45 (0.42), residues: 150
  loop : -1.39 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7505)
  covalent geometry    : angle       0.54501 (10157)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       0.48169 (    2)
  hydrogen bonds       : bond        0.03896 (  363)
  hydrogen bonds       : angle       4.34218 ( 1059)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7062 (tpp-160) cc_final: 0.6564 (mmm160)
REVERT: A   60 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7023 (mpp)
REVERT: A  211 LYS cc_start: 0.7780 (pttm) cc_final: 0.7398 (ptpt)
REVERT: A  278 ASN cc_start: 0.7286 (m-40) cc_final: 0.6902 (m-40)
REVERT: A  283 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6910 (tpt90)
REVERT: A  309 GLU cc_start: 0.6600 (tp30) cc_final: 0.6097 (mm-30)
REVERT: B   99 TRP cc_start: 0.6682 (m100) cc_final: 0.6235 (m100)
REVERT: B  134 ARG cc_start: 0.8226 (ptp-110) cc_final: 0.7661 (ptm160)
REVERT: B  225 HIS cc_start: 0.4981 (OUTLIER) cc_final: 0.4328 (m-70)
REVERT: R   90 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4357 (m-10)
REVERT: R  196 MET cc_start: 0.7677 (mmt) cc_final: 0.7425 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0758
  time to fit residues: 11.3466
Evaluate side-chains
  114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue   51 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0010
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0270
   chunk 55 optimal weight:    0.0010
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.2450

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.258535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.198708 restraints weight = 8051.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.4348 rms_B_bonded: 2.97
r_work: 0.4197 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7506  Z= 0.104
  Angle     :  0.533  10.865  10159  Z= 0.275
  Chirality :  0.041   0.147   1136
  Planarity :  0.003   0.050   1284
  Dihedral  :  5.419  59.129   1021
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.74 %
    Favored  : 78.99 %
  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 aren not related in a simple way.
  whole:  0.47 (0.29), residues: 909
  helix:  2.10 (0.27), residues: 389
  sheet: -0.41 (0.43), residues: 145
  loop : -1.37 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 134 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 7505)
  covalent geometry    : angle       0.53315 (10157)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.39397 (    2)
  hydrogen bonds       : bond        0.03705 (  363)
  hydrogen bonds       : angle       4.29101 ( 1059)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1822.25 seconds
wall clock time: 31 minutes 48.07 seconds (1908.07 seconds total)