Starting phenix.real_space_refine
on Fri Mar 14 06:02:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hnk_34914/03_2025/8hnk_34914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hnk_34914/03_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_34914/03_2025/8hnk_34914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hnk_34914/03_2025/8hnk_34914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hnk_34914/03_2025/8hnk_34914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hnk_34914/03_2025/8hnk_34914.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.26, per 1000 atoms: 0.66
  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: 2.54
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.13
  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: 2.79

  Time building geometry restraints manager: 2.99 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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.210
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.410
-------------------------------------------------------------------------------
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   9686  Z= 0.246
  Angle     :  0.609   8.121  13119  Z= 0.341
  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 : 8.10
  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 (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:  0.15 (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
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 237 
 PHE   0.015   0.001   PHE R 207 
 TYR   0.034   0.002   TYR S 235 
 ARG   0.006   0.000   ARG B 197 

*********************** 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  : 1.109 
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: 0.2556
  time to fit residues: 51.8572
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  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0060
   chunk 49 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.7398

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.141296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.094387 restraints weight = 13620.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.39
r_work: 0.3129 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9686  Z= 0.184
  Angle     :  0.569   7.551  13119  Z= 0.296
  Chirality :  0.043   0.213   1499
  Planarity :  0.004   0.059   1651
  Dihedral  :  5.479  64.867   1441
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.89 %
    Favored  : 91.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.48 (0.25), residues: 1192
  helix:  1.69 (0.26), residues: 418
  sheet:  0.34 (0.31), residues: 289
  loop : -0.89 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R  47 
 TYR   0.032   0.001   TYR S 235 
 ARG   0.003   0.000   ARG B 197 

*********************** 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
  138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 1.266 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.9021 (tp) cc_final: 0.8727 (tp)
REVERT: G   58 GLU cc_start: 0.8440 (pm20) cc_final: 0.8229 (pm20)
REVERT: R   68 LEU cc_start: 0.8815 (mm) cc_final: 0.8418 (mm)
REVERT: S    6 GLU cc_start: 0.8288 (mp0) cc_final: 0.7606 (mt-10)
  outliers start: 9
  outliers final: 7
  residues processed: 135
  average time/residue: 0.2527
  time to fit residues: 46.5223
Evaluate side-chains
  131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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 100 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0770
   chunk 34 optimal weight:    0.0870
   chunk 55 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.9518

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.140678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.093427 restraints weight = 13667.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.40
r_work: 0.3064 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9686  Z= 0.198
  Angle     :  0.541   7.948  13119  Z= 0.283
  Chirality :  0.043   0.223   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.138  63.171   1441
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.06 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.62 (0.25), residues: 1192
  helix:  1.83 (0.26), residues: 417
  sheet:  0.50 (0.31), residues: 275
  loop : -0.85 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R  47 
 TYR   0.033   0.001   TYR S 235 
 ARG   0.003   0.000   ARG S 218 

*********************** 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
  142 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.999 
Fit side-chains
REVERT: G   36 ASP cc_start: 0.8519 (m-30) cc_final: 0.8014 (m-30)
REVERT: G   51 LEU cc_start: 0.8999 (tp) cc_final: 0.8710 (tp)
REVERT: G   58 GLU cc_start: 0.8484 (pm20) cc_final: 0.8195 (pm20)
REVERT: R   68 LEU cc_start: 0.8853 (mm) cc_final: 0.8459 (mm)
REVERT: S    6 GLU cc_start: 0.8304 (mp0) cc_final: 0.7517 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 135
  average time/residue: 0.2390
  time to fit residues: 43.8855
Evaluate side-chains
  128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
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 105 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 91 optimal weight:   20.0000
   chunk 78 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.141277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.094091 restraints weight = 13509.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.39
r_work: 0.3074 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9686  Z= 0.172
  Angle     :  0.524   8.138  13119  Z= 0.271
  Chirality :  0.042   0.215   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.038  61.908   1441
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.84 %
    Favored  : 88.30 %
  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:  0.73 (0.25), residues: 1192
  helix:  1.96 (0.26), residues: 417
  sheet:  0.51 (0.31), residues: 278
  loop : -0.80 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.031   0.001   TYR S 235 
 ARG   0.002   0.000   ARG S  38 

*********************** 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
  143 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.861 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.8998 (tp) cc_final: 0.8700 (tp)
REVERT: G   58 GLU cc_start: 0.8424 (pm20) cc_final: 0.8122 (pm20)
REVERT: R   68 LEU cc_start: 0.8848 (mm) cc_final: 0.8447 (mm)
REVERT: R  334 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6093 (tp)
REVERT: S  201 ASP cc_start: 0.8689 (t70) cc_final: 0.8349 (t0)
REVERT: S  220 GLU cc_start: 0.7945 (mp0) cc_final: 0.7695 (mp0)
REVERT: S  235 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.7005 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 137
  average time/residue: 0.2457
  time to fit residues: 46.5755
Evaluate side-chains
  130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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 R residue  334 LEU
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 91 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 110 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 111 optimal weight:    0.2980
   chunk 117 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.140424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.093167 restraints weight = 13468.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.39
r_work: 0.3088 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9686  Z= 0.202
  Angle     :  0.530   8.981  13119  Z= 0.275
  Chirality :  0.042   0.224   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.032  62.247   1441
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.72 %
    Favored  : 87.04 %
  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:  0.75 (0.25), residues: 1192
  helix:  1.99 (0.26), residues: 417
  sheet:  0.44 (0.31), residues: 280
  loop : -0.75 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R  47 
 TYR   0.034   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 

*********************** 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
  147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.090 
Fit side-chains
REVERT: G   21 MET cc_start: 0.8591 (tmm) cc_final: 0.8309 (tpp)
REVERT: G   24 ASN cc_start: 0.8629 (t0) cc_final: 0.8409 (t0)
REVERT: G   51 LEU cc_start: 0.9019 (tp) cc_final: 0.8733 (tp)
REVERT: G   58 GLU cc_start: 0.8457 (pm20) cc_final: 0.8149 (pm20)
REVERT: R   68 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: S  201 ASP cc_start: 0.8700 (t70) cc_final: 0.8405 (t0)
REVERT: S  235 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7123 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2285
  time to fit residues: 43.6343
Evaluate side-chains
  134 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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  329 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain S residue    7 SER
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 44 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.138156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.090465 restraints weight = 13542.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.38
r_work: 0.3069 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9686  Z= 0.299
  Angle     :  0.590  11.459  13119  Z= 0.303
  Chirality :  0.044   0.266   1499
  Planarity :  0.004   0.059   1651
  Dihedral  :  5.244  64.479   1441
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.60 %
    Favored  : 85.77 %
  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:  0.67 (0.25), residues: 1192
  helix:  1.85 (0.26), residues: 417
  sheet:  0.44 (0.31), residues: 282
  loop : -0.77 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.043   0.002   TYR S 235 
 ARG   0.002   0.000   ARG A  21 

*********************** 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
  149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 1.069 
Fit side-chains
REVERT: G   58 GLU cc_start: 0.8547 (pm20) cc_final: 0.8164 (pm20)
REVERT: R   68 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: R  334 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6226 (tp)
REVERT: S  201 ASP cc_start: 0.8729 (t70) cc_final: 0.8476 (t0)
REVERT: S  235 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7286 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 142
  average time/residue: 0.2093
  time to fit residues: 42.1551
Evaluate side-chains
  143 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
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 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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 8 optimal weight:    0.0070
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0030
   chunk 47 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.9210

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.140187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.092865 restraints weight = 13615.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.39
r_work: 0.3104 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9686  Z= 0.187
  Angle     :  0.543  10.885  13119  Z= 0.279
  Chirality :  0.042   0.215   1499
  Planarity :  0.004   0.058   1651
  Dihedral  :  5.115  62.676   1441
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.67 %
    Favored  : 85.09 %
  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:  0.75 (0.25), residues: 1192
  helix:  1.98 (0.26), residues: 417
  sheet:  0.49 (0.31), residues: 278
  loop : -0.77 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 237 
 PHE   0.017   0.001   PHE R  47 
 TYR   0.033   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 

*********************** 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: 23
    poor density    : 121
  time to evaluate  : 1.000 
Fit side-chains
REVERT: G   51 LEU cc_start: 0.9048 (tp) cc_final: 0.8771 (tp)
REVERT: G   58 GLU cc_start: 0.8500 (pm20) cc_final: 0.8143 (pm20)
REVERT: R   68 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8466 (mm)
REVERT: R  281 MET cc_start: 0.6391 (tmm) cc_final: 0.5961 (tmm)
REVERT: R  334 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6341 (tp)
REVERT: S  201 ASP cc_start: 0.8696 (t70) cc_final: 0.8431 (t0)
REVERT: S  235 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7038 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2162
  time to fit residues: 41.6796
Evaluate side-chains
  136 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
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   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   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 72 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0970
   chunk 0 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0980
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.142265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.095148 restraints weight = 13637.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.39
r_work: 0.3141 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9686  Z= 0.147
  Angle     :  0.518  10.856  13119  Z= 0.265
  Chirality :  0.041   0.187   1499
  Planarity :  0.004   0.057   1651
  Dihedral  :  4.929  60.636   1441
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.87 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.88 (0.25), residues: 1192
  helix:  2.14 (0.26), residues: 418
  sheet:  0.58 (0.31), residues: 276
  loop : -0.78 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.000   HIS R 237 
 PHE   0.016   0.001   PHE R  47 
 TYR   0.027   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 

*********************** 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: 23
    poor density    : 117
  time to evaluate  : 1.037 
Fit side-chains
REVERT: B  318 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8860 (tt)
REVERT: G   51 LEU cc_start: 0.9044 (tp) cc_final: 0.8768 (tp)
REVERT: G   58 GLU cc_start: 0.8320 (pm20) cc_final: 0.8013 (pm20)
REVERT: R   68 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8500 (mm)
REVERT: R  281 MET cc_start: 0.6534 (tmm) cc_final: 0.6061 (tmm)
REVERT: R  334 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6245 (tp)
REVERT: S  201 ASP cc_start: 0.8674 (t70) cc_final: 0.8430 (t0)
REVERT: S  235 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6834 (t80)
  outliers start: 23
  outliers final: 13
  residues processed: 133
  average time/residue: 0.2174
  time to fit residues: 40.9685
Evaluate side-chains
  130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
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  318 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
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  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 96 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
G  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.141102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.093781 restraints weight = 13580.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.39
r_work: 0.3123 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9686  Z= 0.175
  Angle     :  0.524  10.490  13119  Z= 0.272
  Chirality :  0.042   0.205   1499
  Planarity :  0.004   0.057   1651
  Dihedral  :  4.944  61.124   1441
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.55 %
    Favored  : 84.50 %
  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:  0.89 (0.25), residues: 1192
  helix:  2.15 (0.26), residues: 417
  sheet:  0.55 (0.31), residues: 279
  loop : -0.74 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R  47 
 TYR   0.031   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 

*********************** 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
  136 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.084 
Fit side-chains
REVERT: B  318 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8991 (tt)
REVERT: G   51 LEU cc_start: 0.9035 (tp) cc_final: 0.8755 (tp)
REVERT: G   58 GLU cc_start: 0.8347 (pm20) cc_final: 0.8025 (pm20)
REVERT: R   68 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8494 (mm)
REVERT: R  334 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6244 (tp)
REVERT: S  201 ASP cc_start: 0.8676 (t70) cc_final: 0.8453 (t0)
REVERT: S  235 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6982 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 130
  average time/residue: 0.2168
  time to fit residues: 39.8228
Evaluate side-chains
  129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
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  318 LEU
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
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  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 91 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 107 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
G  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.140353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.092891 restraints weight = 13740.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.40
r_work: 0.3107 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
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      :  0.003   0.032   9686  Z= 0.209
  Angle     :  0.552  10.435  13119  Z= 0.282
  Chirality :  0.043   0.262   1499
  Planarity :  0.004   0.057   1651
  Dihedral  :  4.990  61.630   1441
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.45 %
    Favored  : 84.50 %
  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:  0.87 (0.25), residues: 1192
  helix:  2.11 (0.26), residues: 417
  sheet:  0.56 (0.31), residues: 279
  loop : -0.74 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.021   0.001   PHE R  47 
 TYR   0.035   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 

********************** 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
  134 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 1.107 
Fit side-chains
REVERT: B  318 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8984 (tt)
REVERT: G   51 LEU cc_start: 0.9050 (tp) cc_final: 0.8767 (tp)
REVERT: G   58 GLU cc_start: 0.8382 (pm20) cc_final: 0.8052 (pm20)
REVERT: R   68 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8499 (mm)
REVERT: R  281 MET cc_start: 0.6457 (tmm) cc_final: 0.6019 (tmm)
REVERT: R  334 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6287 (tp)
REVERT: S  201 ASP cc_start: 0.8680 (t70) cc_final: 0.8468 (t0)
REVERT: S  235 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7058 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 128
  average time/residue: 0.2217
  time to fit residues: 40.2144
Evaluate side-chains
  130 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
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 B residue  318 LEU
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   68 LEU
Chi-restraints excluded: chain R residue  111 VAL
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  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 38 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 117 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0770
   chunk 99 optimal weight:    0.2980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
G  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.140566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.093148 restraints weight = 13619.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.40
r_work: 0.3111 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.121   9686  Z= 0.226
  Angle     :  0.988  59.195  13119  Z= 0.596
  Chirality :  0.045   0.447   1499
  Planarity :  0.005   0.139   1651
  Dihedral  :  5.137  61.605   1441
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.94 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.85 (0.25), residues: 1192
  helix:  2.07 (0.26), residues: 418
  sheet:  0.55 (0.31), residues: 279
  loop : -0.74 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R  47 
 TYR   0.035   0.001   TYR S 235 
 ARG   0.002   0.000   ARG B  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6848.98 seconds
wall clock time: 118 minutes 24.34 seconds (7104.34 seconds total)