Starting phenix.real_space_refine
on Wed Mar 12 04:30:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlp_36403/03_2025/8jlp_36403.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlp_36403/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlp_36403/03_2025/8jlp_36403.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlp_36403/03_2025/8jlp_36403.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlp_36403/03_2025/8jlp_36403.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlp_36403/03_2025/8jlp_36403.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 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: 4.73, per 1000 atoms: 0.64
  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: 1.73
  Conformation dependent library (CDL) restraints added in 944.2 milliseconds
  

  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: 0.76
  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: 2.10

  Time building geometry restraints manager: 1.98 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:             0.990
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.930
-------------------------------------------------------------------------------
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   7505  Z= 0.222
  Angle     :  0.635   9.570  10157  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (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
 TRP   0.022   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.013   0.002   PHE R 165 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.004   0.000   ARG A 283 

*********************** 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  : 0.733 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1941
  time to fit residues: 31.1295
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  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:    0.2980
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4793 r_free = 0.4793 target = 0.247377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.189569 restraints weight = 7881.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.4291 rms_B_bonded: 3.13
r_work: 0.4078 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7505  Z= 0.283
  Angle     :  0.636   7.588  10157  Z= 0.335
  Chirality :  0.044   0.141   1136
  Planarity :  0.004   0.050   1284
  Dihedral  :  6.943  84.703   1021
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.56 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.29), residues: 909
  helix:  1.46 (0.26), residues: 396
  sheet: -1.05 (0.40), residues: 172
  loop : -1.54 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS Y  44 
 PHE   0.022   0.002   PHE R 154 
 TYR   0.017   0.001   TYR A  37 
 ARG   0.003   0.000   ARG A 283 

*********************** 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
  114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A  344 GLU cc_start: 0.7931 (pm20) cc_final: 0.7634 (pm20)
REVERT: R  178 CYS cc_start: 0.8317 (m) cc_final: 0.8090 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 109
  average time/residue: 0.1869
  time to fit residues: 28.1004
Evaluate side-chains
  105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  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 R residue  194 THR
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  259 VAL
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 89 optimal weight:    0.0170
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 ** 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 = 0.4829 r_free = 0.4829 target = 0.252743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.192473 restraints weight = 8183.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4322 rms_B_bonded: 2.94
r_work: 0.4160 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7505  Z= 0.157
  Angle     :  0.534   8.363  10157  Z= 0.282
  Chirality :  0.041   0.143   1136
  Planarity :  0.004   0.050   1284
  Dihedral  :  6.366  79.124   1021
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.08 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.29), residues: 909
  helix:  1.77 (0.27), residues: 396
  sheet: -0.89 (0.42), residues: 154
  loop : -1.46 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.023   0.001   PHE R 154 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.002   0.000   ARG A 265 

*********************** 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
  113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7339 (mpp) cc_final: 0.6726 (mpp)
REVERT: A  211 LYS cc_start: 0.7679 (pttm) cc_final: 0.7340 (ptpt)
REVERT: A  278 ASN cc_start: 0.7358 (m-40) cc_final: 0.7074 (m-40)
REVERT: A  344 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7577 (pm20)
REVERT: R  196 MET cc_start: 0.7587 (mmt) cc_final: 0.7335 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1991
  time to fit residues: 29.2850
Evaluate side-chains
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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  372 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue  194 THR
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 68 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.250120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.202628 restraints weight = 8201.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.4424 rms_B_bonded: 2.81
r_work: 0.4136 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7505  Z= 0.202
  Angle     :  0.550   7.147  10157  Z= 0.289
  Chirality :  0.042   0.146   1136
  Planarity :  0.004   0.048   1284
  Dihedral  :  6.307  79.492   1021
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.72 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.29), residues: 909
  helix:  1.77 (0.27), residues: 396
  sheet: -0.86 (0.42), residues: 154
  loop : -1.43 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  55 
 PHE   0.020   0.001   PHE R 154 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.003   0.000   ARG A  20 

*********************** 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
  118 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7372 (mpp) cc_final: 0.6849 (mpp)
REVERT: A  211 LYS cc_start: 0.7695 (pttm) cc_final: 0.7349 (ptpt)
REVERT: A  278 ASN cc_start: 0.7478 (m-40) cc_final: 0.7187 (m-40)
REVERT: B   45 MET cc_start: 0.7305 (mtm) cc_final: 0.7066 (ttm)
  outliers start: 16
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1892
  time to fit residues: 29.0146
Evaluate side-chains
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  344 GLU
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 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 73 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   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 225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.251338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.190203 restraints weight = 8098.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 3.00
r_work: 0.4145 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7505  Z= 0.163
  Angle     :  0.524   8.645  10157  Z= 0.277
  Chirality :  0.041   0.139   1136
  Planarity :  0.003   0.047   1284
  Dihedral  :  6.088  76.204   1021
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.72 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.29), residues: 909
  helix:  1.96 (0.27), residues: 390
  sheet: -0.81 (0.43), residues: 149
  loop : -1.40 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 113 
 PHE   0.013   0.001   PHE A 290 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.004   0.000   ARG A  20 

*********************** 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
  116 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7417 (mpp) cc_final: 0.6933 (mpp)
REVERT: A  211 LYS cc_start: 0.7639 (pttm) cc_final: 0.7254 (ptpt)
REVERT: A  244 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: A  278 ASN cc_start: 0.7369 (m-40) cc_final: 0.7040 (m-40)
REVERT: A  289 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7722 (tt)
REVERT: B  225 HIS cc_start: 0.5041 (OUTLIER) cc_final: 0.4359 (m-70)
REVERT: R  196 MET cc_start: 0.7594 (mmt) cc_final: 0.7329 (mmm)
  outliers start: 20
  outliers final: 13
  residues processed: 112
  average time/residue: 0.2064
  time to fit residues: 31.8711
Evaluate side-chains
  110 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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  290 PHE
Chi-restraints excluded: chain A residue  344 GLU
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 R residue   56 THR
Chi-restraints excluded: chain R residue  126 CYS
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 68 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.244741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.188852 restraints weight = 7992.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 2.97
r_work: 0.4073 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7505  Z= 0.307
  Angle     :  0.609   7.388  10157  Z= 0.322
  Chirality :  0.044   0.150   1136
  Planarity :  0.004   0.046   1284
  Dihedral  :  6.659  83.576   1021
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.23 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.29), residues: 909
  helix:  1.62 (0.26), residues: 397
  sheet: -1.01 (0.42), residues: 157
  loop : -1.40 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.013   0.001   HIS B 225 
 PHE   0.017   0.002   PHE A 290 
 TYR   0.019   0.002   TYR A  37 
 ARG   0.006   0.000   ARG A  20 

*********************** 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
  123 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7482 (mpp) cc_final: 0.7042 (mpp)
REVERT: A  221 MET cc_start: 0.7030 (mmt) cc_final: 0.6736 (mmt)
REVERT: A  244 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7842 (mp)
REVERT: A  278 ASN cc_start: 0.7550 (m-40) cc_final: 0.7225 (m-40)
REVERT: A  283 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.6943 (tpt90)
REVERT: B   99 TRP cc_start: 0.6739 (m100) cc_final: 0.6374 (m100)
  outliers start: 25
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1842
  time to fit residues: 29.1796
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  : 0.788 
-------------------------------------------------------------------------------
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  290 PHE
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
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  250 CYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain R residue   51 PHE
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  126 CYS
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 67 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0570
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0030
   chunk 21 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4308

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** R  50 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 = 0.4821 r_free = 0.4821 target = 0.251231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.190260 restraints weight = 7991.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.4310 rms_B_bonded: 2.96
r_work: 0.4148 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7505  Z= 0.151
  Angle     :  0.542  11.440  10157  Z= 0.282
  Chirality :  0.041   0.209   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.328  77.939   1021
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.36 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 909
  helix:  1.89 (0.27), residues: 390
  sheet: -0.78 (0.42), residues: 159
  loop : -1.40 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  55 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.003   0.000   ARG R  83 

*********************** 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
  115 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7106 (tpp-160) cc_final: 0.6604 (mmm160)
REVERT: A   60 MET cc_start: 0.7498 (mpp) cc_final: 0.6429 (mpp)
REVERT: A  211 LYS cc_start: 0.7642 (pttm) cc_final: 0.7223 (ptpt)
REVERT: A  244 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7803 (mt)
REVERT: A  278 ASN cc_start: 0.7378 (m-40) cc_final: 0.7023 (m-40)
REVERT: A  309 GLU cc_start: 0.6489 (tp30) cc_final: 0.5878 (mm-30)
REVERT: B   99 TRP cc_start: 0.6715 (m100) cc_final: 0.6300 (m100)
REVERT: R  196 MET cc_start: 0.7616 (mmt) cc_final: 0.7354 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2931
  time to fit residues: 44.9308
Evaluate side-chains
  107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
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  344 GLU
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  276 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  284 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4820 r_free = 0.4820 target = 0.250782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.189680 restraints weight = 8026.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 2.94
r_work: 0.4139 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7505  Z= 0.164
  Angle     :  0.540   9.256  10157  Z= 0.281
  Chirality :  0.042   0.242   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.204  75.569   1021
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.87 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.29), residues: 909
  helix:  1.96 (0.26), residues: 390
  sheet: -0.78 (0.42), residues: 154
  loop : -1.38 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R  55 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.002   0.000   ARG A  20 

*********************** 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
  124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.6642 (mmm160)
REVERT: A   60 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7064 (mpp)
REVERT: A  211 LYS cc_start: 0.7637 (pttm) cc_final: 0.7211 (ptpt)
REVERT: A  244 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7835 (mp)
REVERT: A  278 ASN cc_start: 0.7372 (m-40) cc_final: 0.7007 (m-40)
REVERT: A  309 GLU cc_start: 0.6540 (tp30) cc_final: 0.5964 (mm-30)
REVERT: B   99 TRP cc_start: 0.6665 (m100) cc_final: 0.6251 (m100)
REVERT: R   90 TYR cc_start: 0.4902 (OUTLIER) cc_final: 0.4354 (m-10)
REVERT: R  196 MET cc_start: 0.7610 (mmt) cc_final: 0.7346 (mmm)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1872
  time to fit residues: 29.5629
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  290 PHE
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   90 VAL
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 B residue  284 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0040
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.8596

-------------------------------------------------------------------------------
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 = 0.4817 r_free = 0.4817 target = 0.250794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.189456 restraints weight = 8055.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.4292 rms_B_bonded: 2.97
r_work: 0.4132 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7505  Z= 0.174
  Angle     :  0.543   9.653  10157  Z= 0.283
  Chirality :  0.041   0.173   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.203  75.209   1021
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.12 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.29), residues: 909
  helix:  2.00 (0.27), residues: 390
  sheet: -0.77 (0.42), residues: 154
  loop : -1.39 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R  55 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.006   0.000   ARG B 134 

*********************** 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
  124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7022 (mpp)
REVERT: A  211 LYS cc_start: 0.7614 (pttm) cc_final: 0.7179 (ptpt)
REVERT: A  221 MET cc_start: 0.7192 (mmt) cc_final: 0.6862 (mmt)
REVERT: A  244 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7845 (mp)
REVERT: A  278 ASN cc_start: 0.7391 (m-40) cc_final: 0.7008 (m-40)
REVERT: A  283 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.6866 (tpt90)
REVERT: A  309 GLU cc_start: 0.6511 (tp30) cc_final: 0.5931 (mm-30)
REVERT: B   99 TRP cc_start: 0.6658 (m100) cc_final: 0.6252 (m100)
REVERT: B  134 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7647 (ptm160)
REVERT: B  199 PHE cc_start: 0.6749 (p90) cc_final: 0.6539 (p90)
REVERT: R   90 TYR cc_start: 0.4941 (OUTLIER) cc_final: 0.4405 (m-10)
REVERT: R  196 MET cc_start: 0.7599 (mmt) cc_final: 0.7337 (mmm)
  outliers start: 25
  outliers final: 20
  residues processed: 116
  average time/residue: 0.2166
  time to fit residues: 33.4236
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  : 0.753 
-------------------------------------------------------------------------------
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  290 PHE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   47 THR
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  276 VAL
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  284 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.0570
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 10 optimal weight:   40.0000
   overall best weight:    1.3102

-------------------------------------------------------------------------------
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 = 0.4801 r_free = 0.4801 target = 0.248654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.200019 restraints weight = 8099.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4399 rms_B_bonded: 3.06
r_work: 0.4106 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7505  Z= 0.218
  Angle     :  0.570   9.578  10157  Z= 0.299
  Chirality :  0.042   0.174   1136
  Planarity :  0.004   0.047   1284
  Dihedral  :  6.492  79.777   1021
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.50 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.29), residues: 909
  helix:  1.86 (0.26), residues: 390
  sheet: -0.79 (0.42), residues: 159
  loop : -1.38 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R  55 
 PHE   0.015   0.001   PHE A 290 
 TYR   0.013   0.001   TYR A  37 
 ARG   0.005   0.000   ARG B 134 

********************** 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
  123 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7203 (tpp-160) cc_final: 0.6690 (mmm160)
REVERT: A   60 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7056 (mpp)
REVERT: A  211 LYS cc_start: 0.7633 (pttm) cc_final: 0.7225 (ptpt)
REVERT: A  221 MET cc_start: 0.7257 (mmt) cc_final: 0.6996 (mmt)
REVERT: A  244 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7863 (mp)
REVERT: A  278 ASN cc_start: 0.7556 (m-40) cc_final: 0.7190 (m-40)
REVERT: A  283 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6944 (tpt90)
REVERT: A  309 GLU cc_start: 0.6449 (tp30) cc_final: 0.5832 (mm-30)
REVERT: B  134 ARG cc_start: 0.8301 (ptp-110) cc_final: 0.7375 (ptp90)
REVERT: B  199 PHE cc_start: 0.6902 (p90) cc_final: 0.6675 (p90)
  outliers start: 23
  outliers final: 19
  residues processed: 117
  average time/residue: 0.3401
  time to fit residues: 52.4527
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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  290 PHE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  178 THR
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 B residue  284 LEU
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 86 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 81 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.249862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.201806 restraints weight = 8084.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.4409 rms_B_bonded: 2.98
r_work: 0.4116 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7505  Z= 0.190
  Angle     :  0.556   9.805  10157  Z= 0.290
  Chirality :  0.042   0.149   1136
  Planarity :  0.003   0.048   1284
  Dihedral  :  6.550  79.628   1021
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.62 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.29), residues: 909
  helix:  1.93 (0.26), residues: 390
  sheet: -0.76 (0.42), residues: 154
  loop : -1.41 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.003   0.001   HIS R  55 
 PHE   0.018   0.001   PHE R  51 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.005   0.000   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4574.88 seconds
wall clock time: 82 minutes 47.40 seconds (4967.40 seconds total)