Starting phenix.real_space_refine
on Sat Aug 23 04:13:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hnk_34914/08_2025/8hnk_34914.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      70      5.16       5
     C    6050      2.51       5
     N    1635      2.21       5
     O    1737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 9492
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1758
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "R"
      Number of atoms: 2316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2316
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 12, 'TRANS': 284}
    Chain: "L"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 578
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 4, 'TRANS': 68}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.21
  Number of scatterers: 9492
  At special positions: 0
  Unit cell: (94.35, 121.55, 147.05, 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      70     16.00
     O    1737      8.00
     N    1635      7.00
     C    6050      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  43 " - pdb=" SG  CYS R 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 124 " - pdb=" SG  CYS R 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   9 " - pdb=" SG  CYS L  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  11 " - pdb=" SG  CYS L  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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: 0.88
  Conformation dependent library (CDL) restraints added in 256.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2258

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 15 sheets defined
      37.5% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 31
      removed outlier: 3.663A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.078A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 4.558A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.560A  pdb=" N   GLU G  58 " --> pdb=" O   PRO G  55 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 55 through 59'
    Processing helix  chain 'R' and resid 45 through 81
      removed outlier: 3.598A  pdb=" N   LEU R  49 " --> pdb=" O   GLN R  45 " (cutoff:3.500A)
      Proline residue:  R  57  - end of helix
      removed outlier: 3.968A  pdb=" N   ARG R  81 " --> pdb=" O   VAL R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 115
      Proline residue:  R 107  - end of helix
    Processing helix  chain 'R' and resid 121 through 154
    Processing helix  chain 'R' and resid 155 through 163
    Processing helix  chain 'R' and resid 166 through 190
      removed outlier: 3.590A  pdb=" N   LEU R 170 " --> pdb=" O   ALA R 166 " (cutoff:3.500A)
      Proline residue:  R 185  - end of helix
    Processing helix  chain 'R' and resid 208 through 245
      removed outlier: 5.748A  pdb=" N   LEU R 226 " --> pdb=" O   ALA R 222 " (cutoff:3.500A)
      Proline residue:  R 227  - end of helix
    Processing helix  chain 'R' and resid 249 through 284
      Proline residue:  R 270  - end of helix
    Processing helix  chain 'R' and resid 289 through 319
      Proline residue:  R 315  - end of helix
    Processing helix  chain 'R' and resid 322 through 334
    Processing helix  chain 'L' and resid 46 through 49
    Processing helix  chain 'L' and resid 58 through 72
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.558A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.041A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.654A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.137A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.325A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.507A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.903A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.831A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.932A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 5.928A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.680A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 191 through 195
      removed outlier: 4.171A  pdb=" N   ALA R 200 " --> pdb=" O   ASP R 195 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 27 through 30
      removed outlier: 4.246A  pdb=" N   VAL L  41 " --> pdb=" O   LEU L  54 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.951A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.951A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.561A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    489 hydrogen bonds defined for protein.
    1383 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: 1.55

  Time building geometry restraints manager: 1.14 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: 3071
        1.34 -     1.46: 2206
        1.46 -     1.58: 4309
        1.58 -     1.70: 1
        1.70 -     1.82: 99
  Bond restraints: 9686
  Sorted by residual:
  bond pdb=" N   ASP R 282 "
       pdb=" CA  ASP R 282 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.23e-02 6.61e+03 4.35e+00
  bond pdb=" CB  PRO S 148 "
       pdb=" CG  PRO S 148 "
    ideal  model  delta    sigma   weight residual
    1.492  1.582 -0.090 5.00e-02 4.00e+02 3.21e+00
  bond pdb=" N   ARG L   6 "
       pdb=" CA  ARG L   6 "
    ideal  model  delta    sigma   weight residual
    1.455  1.473 -0.019 1.27e-02 6.20e+03 2.16e+00
  bond pdb=" CB  CYS B 114 "
       pdb=" SG  CYS B 114 "
    ideal  model  delta    sigma   weight residual
    1.808  1.766  0.042 3.30e-02 9.18e+02 1.60e+00
  bond pdb=" C3  CLR R 601 "
       pdb=" O1  CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.10e+00
  ... (remaining 9681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 12809
        1.62 -     3.25: 252
        3.25 -     4.87: 40
        4.87 -     6.50: 14
        6.50 -     8.12: 4
  Bond angle restraints: 13119
  Sorted by residual:
  angle pdb=" CA  TYR S 235 "
        pdb=" CB  TYR S 235 "
        pdb=" CG  TYR S 235 "
      ideal   model   delta    sigma   weight residual
     113.90  107.10    6.80 1.80e+00 3.09e-01 1.43e+01
  angle pdb=" C   LYS L  46 "
        pdb=" N   GLU L  47 "
        pdb=" CA  GLU L  47 "
      ideal   model   delta    sigma   weight residual
     122.61  126.75   -4.14 1.56e+00 4.11e-01 7.05e+00
  angle pdb=" C   MET L  30 "
        pdb=" N   TYR L  31 "
        pdb=" CA  TYR L  31 "
      ideal   model   delta    sigma   weight residual
     121.03  125.15   -4.12 1.60e+00 3.91e-01 6.65e+00
  angle pdb=" CA  ARG L   6 "
        pdb=" C   ARG L   6 "
        pdb=" O   ARG L   6 "
      ideal   model   delta    sigma   weight residual
     121.33  118.56    2.77 1.08e+00 8.57e-01 6.57e+00
  angle pdb=" N   TYR S 235 "
        pdb=" CA  TYR S 235 "
        pdb=" C   TYR S 235 "
      ideal   model   delta    sigma   weight residual
     109.81  115.21   -5.40 2.21e+00 2.05e-01 5.98e+00
  ... (remaining 13114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5333
       17.93 -    35.86: 461
       35.86 -    53.79: 79
       53.79 -    71.72: 12
       71.72 -    89.65: 5
  Dihedral angle restraints: 5890
    sinusoidal: 2392
      harmonic: 3498
  Sorted by residual:
  dihedral pdb=" CB  CYS R  43 "
           pdb=" SG  CYS R  43 "
           pdb=" SG  CYS R 290 "
           pdb=" CB  CYS R 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.22  -79.22     1      1.00e+01 1.00e-02 7.80e+01
  dihedral pdb=" CA  GLU S 234 "
           pdb=" C   GLU S 234 "
           pdb=" N   TYR S 235 "
           pdb=" CA  TYR S 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.05  -20.95     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  SER S 208 "
           pdb=" C   SER S 208 "
           pdb=" N   GLY S 209 "
           pdb=" CA  GLY S 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.92   20.08     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 5887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1112
       0.044 -    0.088: 289
       0.088 -    0.132: 88
       0.132 -    0.176: 7
       0.176 -    0.220: 3
  Chirality restraints: 1499
  Sorted by residual:
  chirality pdb=" CA  ILE L  29 "
            pdb=" N   ILE L  29 "
            pdb=" C   ILE L  29 "
            pdb=" CB  ILE L  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR S 235 "
            pdb=" N   TYR S 235 "
            pdb=" C   TYR S 235 "
            pdb=" CB  TYR S 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.10e-01
  chirality pdb=" CA  LEU R  56 "
            pdb=" N   LEU R  56 "
            pdb=" C   LEU R  56 "
            pdb=" CB  LEU R  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.29e-01
  ... (remaining 1496 not shown)

  Planarity restraints: 1651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.41e+00
        pdb=" N   PRO S  75 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 235 "    0.038 5.00e-02 4.00e+02   5.72e-02 5.24e+00
        pdb=" N   PRO S 236 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO S 236 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO S 236 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 235 "    0.025 2.00e-02 2.50e+03   1.52e-02 4.64e+00
        pdb=" CG  TYR S 235 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 235 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 235 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 235 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 235 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 235 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR S 235 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1648 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 417
        2.72 -     3.27: 9334
        3.27 -     3.81: 14931
        3.81 -     4.36: 18645
        4.36 -     4.90: 33054
  Nonbonded interactions: 76381
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER S  52 "
            pdb=" NH1 ARG S  72 "
     model   vdw
     2.265 3.120
  ... (remaining 76376 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:             1.200
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.120
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
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      :  0.004   0.090   9692  Z= 0.165
  Angle     :  0.610   8.121  13131  Z= 0.342
  Chirality :  0.044   0.220   1499
  Planarity :  0.004   0.063   1651
  Dihedral  : 13.488  89.649   3614
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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:  0.15 (0.24), residues: 1192
  helix:  1.50 (0.26), residues: 407
  sheet:  0.10 (0.31), residues: 287
  loop : -1.05 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.034   0.002   TYR S 235 
 PHE   0.015   0.001   PHE R 207 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9686)
  covalent geometry    : angle       0.60886 (13119)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.29107 (   12)
  hydrogen bonds       : bond        0.12349 (  485)
  hydrogen bonds       : angle       5.40219 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.260 
Fit side-chains
REVERT: R  331 MET cc_start: 0.7491 (ttm) cc_final: 0.7207 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1003
  time to fit residues: 20.2828
Evaluate side-chains
  129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0020
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.142124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.095419 restraints weight = 13687.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.38
r_work: 0.3150 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9692  Z= 0.118
  Angle     :  0.559   7.372  13131  Z= 0.292
  Chirality :  0.043   0.204   1499
  Planarity :  0.004   0.059   1651
  Dihedral  :  5.446  63.206   1441
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.12 %
    Favored  : 92.01 %
  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:  0.50 (0.25), residues: 1192
  helix:  1.73 (0.26), residues: 418
  sheet:  0.39 (0.31), residues: 276
  loop : -0.90 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 197 
 TYR   0.029   0.001   TYR S 235 
 PHE   0.015   0.001   PHE R  47 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9686)
  covalent geometry    : angle       0.55873 (13119)
  SS BOND              : bond        0.00314 (    6)
  SS BOND              : angle       0.90383 (   12)
  hydrogen bonds       : bond        0.04232 (  485)
  hydrogen bonds       : angle       4.47702 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.376 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.8989 (tp) cc_final: 0.8691 (tp)
REVERT: R   68 LEU cc_start: 0.8815 (mm) cc_final: 0.8422 (mm)
REVERT: S    6 GLU cc_start: 0.8257 (mp0) cc_final: 0.7619 (mt-10)
  outliers start: 9
  outliers final: 7
  residues processed: 133
  average time/residue: 0.1196
  time to fit residues: 21.3343
Evaluate side-chains
  128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   42 GLU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 95 optimal weight:    0.4980
   chunk 102 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R  50 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.140523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.093283 restraints weight = 13589.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.40
r_work: 0.3065 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9692  Z= 0.137
  Angle     :  0.548   8.146  13131  Z= 0.286
  Chirality :  0.043   0.226   1499
  Planarity :  0.004   0.059   1651
  Dihedral  :  5.165  63.677   1441
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  8.97 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.25), residues: 1192
  helix:  1.84 (0.26), residues: 417
  sheet:  0.49 (0.31), residues: 277
  loop : -0.85 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S  38 
 TYR   0.035   0.001   TYR S 235 
 PHE   0.016   0.001   PHE R  47 
 TRP   0.009   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9686)
  covalent geometry    : angle       0.54705 (13119)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       0.93341 (   12)
  hydrogen bonds       : bond        0.04074 (  485)
  hydrogen bonds       : angle       4.31676 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.386 
Fit side-chains
REVERT: G   36 ASP cc_start: 0.8524 (m-30) cc_final: 0.8021 (m-30)
REVERT: G   51 LEU cc_start: 0.9012 (tp) cc_final: 0.8716 (tp)
REVERT: R   68 LEU cc_start: 0.8848 (mm) cc_final: 0.8461 (mm)
REVERT: R  281 MET cc_start: 0.6293 (tmm) cc_final: 0.6066 (tmm)
REVERT: S    6 GLU cc_start: 0.8320 (mp0) cc_final: 0.7532 (mt-10)
  outliers start: 14
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1006
  time to fit residues: 19.0288
Evaluate side-chains
  130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   42 GLU
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0020
   chunk 66 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.9390

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.140459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093307 restraints weight = 13665.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.41
r_work: 0.3061 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9692  Z= 0.129
  Angle     :  0.539   8.335  13131  Z= 0.280
  Chirality :  0.042   0.224   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.083  62.464   1441
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.94 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.74 (0.25), residues: 1192
  helix:  1.93 (0.26), residues: 418
  sheet:  0.51 (0.31), residues: 280
  loop : -0.77 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG S  38 
 TYR   0.033   0.001   TYR S 235 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9686)
  covalent geometry    : angle       0.53839 (13119)
  SS BOND              : bond        0.00364 (    6)
  SS BOND              : angle       0.85347 (   12)
  hydrogen bonds       : bond        0.03896 (  485)
  hydrogen bonds       : angle       4.25348 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.374 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.9017 (tp) cc_final: 0.8733 (tp)
REVERT: R   68 LEU cc_start: 0.8857 (mm) cc_final: 0.8453 (mm)
REVERT: R  281 MET cc_start: 0.6082 (tmm) cc_final: 0.5785 (tmm)
REVERT: S  201 ASP cc_start: 0.8692 (t70) cc_final: 0.8351 (t0)
REVERT: S  235 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7039 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1004
  time to fit residues: 19.0067
Evaluate side-chains
  133 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   42 GLU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 107 optimal weight:    0.5980
   chunk 109 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 100 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.140565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093330 restraints weight = 13673.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.40
r_work: 0.3060 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9692  Z= 0.127
  Angle     :  0.529   8.878  13131  Z= 0.276
  Chirality :  0.042   0.220   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.039  62.183   1441
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 10.23 %
    Favored  : 87.23 %
  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:  0.79 (0.25), residues: 1192
  helix:  2.01 (0.26), residues: 417
  sheet:  0.50 (0.31), residues: 278
  loop : -0.75 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  42 
 TYR   0.033   0.001   TYR S 235 
 PHE   0.016   0.001   PHE R  47 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9686)
  covalent geometry    : angle       0.52915 (13119)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       0.78284 (   12)
  hydrogen bonds       : bond        0.03835 (  485)
  hydrogen bonds       : angle       4.24786 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.404 
Fit side-chains
REVERT: G   21 MET cc_start: 0.8581 (tmm) cc_final: 0.8311 (tpp)
REVERT: G   51 LEU cc_start: 0.9010 (tp) cc_final: 0.8738 (tp)
REVERT: R   68 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8478 (mm)
REVERT: R  281 MET cc_start: 0.6139 (tmm) cc_final: 0.5825 (tmm)
REVERT: R  334 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6148 (tp)
REVERT: S  192 MET cc_start: 0.9011 (ttp) cc_final: 0.8765 (tmm)
REVERT: S  201 ASP cc_start: 0.8709 (t70) cc_final: 0.8402 (t0)
REVERT: S  220 GLU cc_start: 0.7990 (mp0) cc_final: 0.7780 (mp0)
REVERT: S  235 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7094 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 139
  average time/residue: 0.1020
  time to fit residues: 19.7021
Evaluate side-chains
  136 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   42 GLU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
R  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.141065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.093935 restraints weight = 13588.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.40
r_work: 0.3068 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
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      :  0.003   0.033   9692  Z= 0.117
  Angle     :  0.530  11.242  13131  Z= 0.271
  Chirality :  0.042   0.209   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  4.980  61.660   1441
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.70 %
    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 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:  0.82 (0.25), residues: 1192
  helix:  2.06 (0.26), residues: 417
  sheet:  0.50 (0.31), residues: 278
  loop : -0.74 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.031   0.001   TYR S 235 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9686)
  covalent geometry    : angle       0.53007 (13119)
  SS BOND              : bond        0.00333 (    6)
  SS BOND              : angle       0.71648 (   12)
  hydrogen bonds       : bond        0.03687 (  485)
  hydrogen bonds       : angle       4.19655 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.312 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.9001 (tp) cc_final: 0.8729 (tp)
REVERT: R   68 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8469 (mm)
REVERT: R  281 MET cc_start: 0.6117 (tmm) cc_final: 0.5500 (tmm)
REVERT: R  334 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6130 (tp)
REVERT: S  201 ASP cc_start: 0.8695 (t70) cc_final: 0.8415 (t0)
REVERT: S  219 LEU cc_start: 0.8525 (mp) cc_final: 0.8313 (mp)
REVERT: S  235 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.7030 (t80)
  outliers start: 22
  outliers final: 13
  residues processed: 133
  average time/residue: 0.1001
  time to fit residues: 18.8278
Evaluate side-chains
  131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0770
   chunk 29 optimal weight:    0.1980
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0030
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.4348

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.142964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.096022 restraints weight = 13628.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.39
r_work: 0.3151 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9692  Z= 0.098
  Angle     :  0.505  10.877  13131  Z= 0.259
  Chirality :  0.041   0.182   1499
  Planarity :  0.004   0.057   1651
  Dihedral  :  4.836  59.744   1441
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.28 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1192
  helix:  2.15 (0.26), residues: 417
  sheet:  0.50 (0.31), residues: 278
  loop : -0.74 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.026   0.001   TYR S 235 
 PHE   0.018   0.001   PHE R  47 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9686)
  covalent geometry    : angle       0.50504 (13119)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       0.66369 (   12)
  hydrogen bonds       : bond        0.03382 (  485)
  hydrogen bonds       : angle       4.09705 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.387 
Fit side-chains
REVERT: B  318 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8833 (tt)
REVERT: G   51 LEU cc_start: 0.8986 (tp) cc_final: 0.8693 (tp)
REVERT: G   58 GLU cc_start: 0.8005 (pm20) cc_final: 0.7577 (pm20)
REVERT: R   68 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8486 (mm)
REVERT: R  281 MET cc_start: 0.6118 (tmm) cc_final: 0.5538 (tmm)
REVERT: S  201 ASP cc_start: 0.8645 (t70) cc_final: 0.8370 (t0)
REVERT: S  235 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6847 (t80)
  outliers start: 22
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1047
  time to fit residues: 19.9103
Evaluate side-chains
  123 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0020
   chunk 27 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 237 ASN
R 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.137219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.089410 restraints weight = 13632.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.38
r_work: 0.3053 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9692  Z= 0.249
  Angle     :  0.633  11.111  13131  Z= 0.323
  Chirality :  0.046   0.281   1499
  Planarity :  0.004   0.059   1651
  Dihedral  :  5.265  64.374   1441
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.06 %
    Favored  : 84.99 %
  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:  0.65 (0.25), residues: 1192
  helix:  1.81 (0.26), residues: 418
  sheet:  0.45 (0.31), residues: 282
  loop : -0.78 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.046   0.002   TYR S 235 
 PHE   0.017   0.002   PHE S  68 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 9686)
  covalent geometry    : angle       0.63230 (13119)
  SS BOND              : bond        0.00475 (    6)
  SS BOND              : angle       1.02135 (   12)
  hydrogen bonds       : bond        0.04623 (  485)
  hydrogen bonds       : angle       4.49313 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8564 (mmm) cc_final: 0.8288 (mmm)
REVERT: G   58 GLU cc_start: 0.8320 (pm20) cc_final: 0.7982 (pm20)
REVERT: R   68 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8441 (mm)
REVERT: R  281 MET cc_start: 0.6224 (tmm) cc_final: 0.5557 (tmm)
REVERT: S  201 ASP cc_start: 0.8777 (t70) cc_final: 0.8523 (t0)
REVERT: S  235 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7518 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 133
  average time/residue: 0.0944
  time to fit residues: 17.7191
Evaluate side-chains
  134 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  204 GLN
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain R residue  329 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 116 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 91 optimal weight:   20.0000
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.140522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.093060 restraints weight = 13552.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.39
r_work: 0.3109 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9692  Z= 0.123
  Angle     :  0.539  10.537  13131  Z= 0.278
  Chirality :  0.042   0.210   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.110  62.516   1441
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.04 %
    Favored  : 84.41 %
  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:  0.75 (0.25), residues: 1192
  helix:  1.98 (0.26), residues: 417
  sheet:  0.57 (0.31), residues: 270
  loop : -0.82 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 246 
 TYR   0.031   0.001   TYR S 235 
 PHE   0.013   0.001   PHE R  47 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9686)
  covalent geometry    : angle       0.53859 (13119)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       0.69391 (   12)
  hydrogen bonds       : bond        0.03809 (  485)
  hydrogen bonds       : angle       4.28363 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8501 (mmm) cc_final: 0.8212 (mmm)
REVERT: G   51 LEU cc_start: 0.9059 (tp) cc_final: 0.8782 (tp)
REVERT: G   58 GLU cc_start: 0.8243 (pm20) cc_final: 0.7920 (pm20)
REVERT: R   68 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8460 (mm)
REVERT: R  281 MET cc_start: 0.6185 (tmm) cc_final: 0.5582 (tmm)
REVERT: S  201 ASP cc_start: 0.8738 (t70) cc_final: 0.8484 (t0)
REVERT: S  235 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6958 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 126
  average time/residue: 0.0912
  time to fit residues: 16.1199
Evaluate side-chains
  128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 116 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.139072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.091342 restraints weight = 13527.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.39
r_work: 0.3083 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9692  Z= 0.170
  Angle     :  0.589  10.934  13131  Z= 0.299
  Chirality :  0.044   0.249   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.165  63.140   1441
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.42 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.25), residues: 1192
  helix:  1.93 (0.26), residues: 417
  sheet:  0.47 (0.31), residues: 282
  loop : -0.75 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG S  38 
 TYR   0.040   0.002   TYR S 235 
 PHE   0.019   0.001   PHE R  47 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9686)
  covalent geometry    : angle       0.58888 (13119)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       0.85274 (   12)
  hydrogen bonds       : bond        0.04100 (  485)
  hydrogen bonds       : angle       4.36409 ( 1383)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  243 MET cc_start: 0.8509 (mmm) cc_final: 0.8234 (mmm)
REVERT: G   36 ASP cc_start: 0.8479 (m-30) cc_final: 0.8033 (m-30)
REVERT: G   58 GLU cc_start: 0.8289 (pm20) cc_final: 0.7934 (pm20)
REVERT: R   68 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8442 (mm)
REVERT: R  281 MET cc_start: 0.6185 (tmm) cc_final: 0.5942 (tmm)
REVERT: S  201 ASP cc_start: 0.8734 (t70) cc_final: 0.8502 (t0)
REVERT: S  235 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7239 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 123
  average time/residue: 0.0939
  time to fit residues: 16.0999
Evaluate side-chains
  127 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  280 LEU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  204 SER
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:    0.1980
   chunk 28 optimal weight:    0.2980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 89 optimal weight:   20.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
R 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.141504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.094078 restraints weight = 13491.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.39
r_work: 0.3123 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9692  Z= 0.108
  Angle     :  0.533  10.298  13131  Z= 0.274
  Chirality :  0.042   0.203   1499
  Planarity :  0.004   0.057   1651
  Dihedral  :  5.041  61.772   1441
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.33 %
    Favored  : 84.02 %
  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:  0.89 (0.25), residues: 1192
  helix:  2.15 (0.26), residues: 412
  sheet:  0.60 (0.31), residues: 276
  loop : -0.73 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.028   0.001   TYR S 235 
 PHE   0.018   0.001   PHE R  47 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.000   HIS R 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9686)
  covalent geometry    : angle       0.53303 (13119)
  SS BOND              : bond        0.00294 (    6)
  SS BOND              : angle       0.67524 (   12)
  hydrogen bonds       : bond        0.03601 (  485)
  hydrogen bonds       : angle       4.22393 ( 1383)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3066.63 seconds
wall clock time: 53 minutes 2.60 seconds (3182.60 seconds total)