Starting phenix.real_space_refine
on Fri Jul 25 05:58:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/07_2025/8h8d_34543.cif"
  }
  resolution = 4.26
  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=  -0.002 sd=   0.054
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      39      5.16       5
     C    4587      2.51       5
     N    1179      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7054
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2366
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 12, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2337
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 12, 'TRANS': 270}
    Chain: "C"
      Number of atoms: 2351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2351
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 12, 'TRANS': 272}
  Time building chain proxies: 4.84, per 1000 atoms: 0.69
  Number of scatterers: 7054
  At special positions: 0
  Unit cell: (80.438, 80.438, 140.223, 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      39     16.00
     O    1249      8.00
     N    1179      7.00
     C    4587      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 129 " - pdb=" SG  CYS C 151 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 887.0 milliseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      34.5% alpha, 28.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 99
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.655A  pdb=" N   PHE A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   CYS A 225 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 304 through 343
    Processing helix  chain 'B' and resid 61 through 97
      removed outlier: 3.689A  pdb=" N   MET B  79 " --> pdb=" O   TYR B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 215
      removed outlier: 3.716A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 213 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 223
    Processing helix  chain 'B' and resid 304 through 342
      removed outlier: 3.789A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 68
    Processing helix  chain 'C' and resid 69 through 99
      removed outlier: 4.051A  pdb=" N   TYR C  75 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 215
    Processing helix  chain 'C' and resid 217 through 229
      removed outlier: 3.521A  pdb=" N   CYS C 225 " --> pdb=" O   PHE C 221 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER C 227 " --> pdb=" O   GLN C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 344
      removed outlier: 3.575A  pdb=" N   ALA C 310 " --> pdb=" O   TRP C 306 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP C 324 " --> pdb=" O   PHE C 320 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 107
      removed outlier: 3.944A  pdb=" N   GLN A 295 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASP A 299 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   HIS A 190 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   LEU A 126 " --> pdb=" O   HIS A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 107
      removed outlier: 3.944A  pdb=" N   GLN A 295 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASP A 299 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG A 261 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155
      removed outlier: 3.716A  pdb=" N   ILE A 172 " --> pdb=" O   GLN A 154 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 201 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 108
      removed outlier: 8.167A  pdb=" N   TYR B 293 " --> pdb=" O   MET B 244 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU B 246 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN B 295 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   ASP B 299 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 154 through 159
      removed outlier: 3.506A  pdb=" N   GLN B 154 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE B 156 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA B 170 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE B 117 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP B 202 " --> pdb=" O   TYR B 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 131
      removed outlier: 3.640A  pdb=" N   HIS B 190 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   GLN B 188 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS B 129 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   PHE B 186 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHE B 238 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE B 284 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 108
      removed outlier: 14.129A  pdb=" N   TYR C 293 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 10.813A  pdb=" N   MET C 244 " --> pdb=" O   TYR C 293 " (cutoff:3.500A)
      removed outlier: 9.958A  pdb=" N   GLN C 295 " --> pdb=" O   MET C 244 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU C 246 " --> pdb=" O   GLN C 295 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ILE C 297 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS C 248 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   THR C 240 " --> pdb=" O   PHE C 284 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN C 188 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER C 128 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   HIS C 190 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   LEU C 126 " --> pdb=" O   HIS C 190 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 108
      removed outlier: 14.129A  pdb=" N   TYR C 293 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 10.813A  pdb=" N   MET C 244 " --> pdb=" O   TYR C 293 " (cutoff:3.500A)
      removed outlier: 9.958A  pdb=" N   GLN C 295 " --> pdb=" O   MET C 244 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU C 246 " --> pdb=" O   GLN C 295 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   ILE C 297 " --> pdb=" O   LEU C 246 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS C 248 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS C 243 " --> pdb=" O   GLU C 263 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 117 through 120
      removed outlier: 4.371A  pdb=" N   ASP C 202 " --> pdb=" O   TYR C 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155
    Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 159

    374 hydrogen bonds defined for protein.
    1062 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: 1.84

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1833
        1.33 -     1.45: 1377
        1.45 -     1.57: 3970
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 7243
  Sorted by residual:
  bond pdb=" CE1 HIS B 340 "
       pdb=" NE2 HIS B 340 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.60e+01
  bond pdb=" N   ILE B 300 "
       pdb=" CA  ILE B 300 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.14e-02 7.69e+03 1.04e+01
  bond pdb=" N   VAL B 330 "
       pdb=" CA  VAL B 330 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.87e+00
  bond pdb=" N   ILE B 301 "
       pdb=" CA  ILE B 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.24e-02 6.50e+03 7.72e+00
  bond pdb=" N   ILE A 301 "
       pdb=" CA  ILE A 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.27e-02 6.20e+03 7.71e+00
  ... (remaining 7238 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 9436
        2.16 -     4.31: 310
        4.31 -     6.47: 32
        6.47 -     8.62: 9
        8.62 -    10.78: 6
  Bond angle restraints: 9793
  Sorted by residual:
  angle pdb=" C   ILE A 159 "
        pdb=" N   ASP A 160 "
        pdb=" CA  ASP A 160 "
      ideal   model   delta    sigma   weight residual
     120.49  131.27  -10.78 1.42e+00 4.96e-01 5.76e+01
  angle pdb=" N   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" C   LYS A 321 "
      ideal   model   delta    sigma   weight residual
     111.36  105.92    5.44 1.09e+00 8.42e-01 2.49e+01
  angle pdb=" CA  ARG B 182 "
        pdb=" CB  ARG B 182 "
        pdb=" CG  ARG B 182 "
      ideal   model   delta    sigma   weight residual
     114.10  123.34   -9.24 2.00e+00 2.50e-01 2.13e+01
  angle pdb=" N   THR B 302 "
        pdb=" CA  THR B 302 "
        pdb=" C   THR B 302 "
      ideal   model   delta    sigma   weight residual
     111.28  115.55   -4.27 1.09e+00 8.42e-01 1.53e+01
  angle pdb=" N   ALA B 303 "
        pdb=" CA  ALA B 303 "
        pdb=" C   ALA B 303 "
      ideal   model   delta    sigma   weight residual
     109.07  115.28   -6.21 1.61e+00 3.86e-01 1.49e+01
  ... (remaining 9788 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3622
       17.90 -    35.81: 530
       35.81 -    53.71: 137
       53.71 -    71.62: 30
       71.62 -    89.52: 13
  Dihedral angle restraints: 4332
    sinusoidal: 1795
      harmonic: 2537
  Sorted by residual:
  dihedral pdb=" CD  ARG B 337 "
           pdb=" NE  ARG B 337 "
           pdb=" CZ  ARG B 337 "
           pdb=" NH1 ARG B 337 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.44   78.44     1      1.00e+01 1.00e-02 7.68e+01
  dihedral pdb=" CB  CYS B 129 "
           pdb=" SG  CYS B 129 "
           pdb=" SG  CYS B 151 "
           pdb=" CB  CYS B 151 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.68   51.32     1      1.00e+01 1.00e-02 3.60e+01
  dihedral pdb=" CD  ARG B 339 "
           pdb=" NE  ARG B 339 "
           pdb=" CZ  ARG B 339 "
           pdb=" NH1 ARG B 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -48.39   48.39     1      1.00e+01 1.00e-02 3.23e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 765
       0.044 -    0.089: 192
       0.089 -    0.133: 76
       0.133 -    0.178: 14
       0.178 -    0.222: 17
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CA  VAL B 315 "
            pdb=" N   VAL B 315 "
            pdb=" C   VAL B 315 "
            pdb=" CB  VAL B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL A 318 "
            pdb=" N   VAL A 318 "
            pdb=" C   VAL A 318 "
            pdb=" CB  VAL A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CB  VAL B 318 "
            pdb=" CA  VAL B 318 "
            pdb=" CG1 VAL B 318 "
            pdb=" CG2 VAL B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1061 not shown)

  Planarity restraints: 1229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 337 "    1.083 9.50e-02 1.11e+02   4.85e-01 1.42e+02
        pdb=" NE  ARG B 337 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 337 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 337 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 337 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 339 "    0.820 9.50e-02 1.11e+02   3.67e-01 8.20e+01
        pdb=" NE  ARG B 339 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 339 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 339 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 339 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 197 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.90e+00
        pdb=" CG  ASP A 197 "   -0.049 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 197 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 197 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1226 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 271
        2.70 -     3.25: 7641
        3.25 -     3.80: 11911
        3.80 -     4.35: 14178
        4.35 -     4.90: 21981
  Nonbonded interactions: 55982
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 197 "
            pdb=" N   PHE A 198 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   ARG B 181 "
            pdb=" NH1 ARG B 181 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   ALA B 211 "
            pdb=" OG  SER B 215 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG1 THR C 302 "
            pdb=" OD1 ASN C 304 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASN B 268 "
            pdb=" N   PHE B 269 "
     model   vdw
     2.232 3.120
  ... (remaining 55977 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 61 through 342)
  selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 77 through 342))
  selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 77 through 342))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.790
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.100
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
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   0.040   7246  Z= 0.282
  Angle     :  0.868  10.779   9799  Z= 0.539
  Chirality :  0.053   0.222   1064
  Planarity :  0.018   0.485   1229
  Dihedral  : 18.367  89.523   2671
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 30.45 %
    Favored  : 64.59 %
  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: -0.02 (0.30), residues: 850
  helix:  1.85 (0.30), residues: 288
  sheet: -0.45 (0.31), residues: 289
  loop : -1.49 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C 133 
 HIS   0.007   0.001   HIS C 132 
 PHE   0.022   0.001   PHE A 320 
 TYR   0.014   0.001   TYR A 120 
 ARG   0.003   0.000   ARG C 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20476 (  357)
  hydrogen bonds       : angle       7.40718 ( 1062)
  SS BOND              : bond        0.00138 (    3)
  SS BOND              : angle       1.81238 (    6)
  covalent geometry    : bond        0.00444 ( 7243)
  covalent geometry    : angle       0.86688 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 MET cc_start: 0.8608 (ptm) cc_final: 0.8395 (ppp)
REVERT: B  325 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9100 (p90)
REVERT: B  338 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4702 (mmm160)
REVERT: B  340 HIS cc_start: -0.2636 (OUTLIER) cc_final: -0.2867 (t-90)
REVERT: C  154 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8426 (tm-30)
  outliers start: 39
  outliers final: 17
  residues processed: 130
  average time/residue: 0.2016
  time to fit residues: 34.7588
Evaluate side-chains
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0010
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 GLN
C 174 GLN
** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.092169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.065768 restraints weight = 26635.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.067391 restraints weight = 16587.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068486 restraints weight = 12337.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7246  Z= 0.175
  Angle     :  0.657   8.185   9799  Z= 0.346
  Chirality :  0.044   0.188   1064
  Planarity :  0.005   0.059   1229
  Dihedral  :  4.861  20.224    928
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.26 (0.30), residues: 850
  helix:  1.30 (0.29), residues: 293
  sheet: -0.43 (0.30), residues: 295
  loop : -1.43 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 232 
 HIS   0.006   0.001   HIS C 190 
 PHE   0.023   0.002   PHE A 320 
 TYR   0.018   0.002   TYR B 158 
 ARG   0.027   0.001   ARG B 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  357)
  hydrogen bonds       : angle       5.39900 ( 1062)
  SS BOND              : bond        0.00309 (    3)
  SS BOND              : angle       1.99922 (    6)
  covalent geometry    : bond        0.00379 ( 7243)
  covalent geometry    : angle       0.65547 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 MET cc_start: 0.8733 (ptm) cc_final: 0.8477 (ppp)
REVERT: B  158 TYR cc_start: 0.8075 (m-10) cc_final: 0.7822 (m-10)
REVERT: B  333 MET cc_start: 0.6750 (tpp) cc_final: 0.6257 (tmm)
REVERT: C   79 MET cc_start: 0.8802 (mmp) cc_final: 0.8510 (mmm)
REVERT: C  112 TYR cc_start: 0.7223 (p90) cc_final: 0.6354 (p90)
REVERT: C  169 HIS cc_start: 0.7779 (t-170) cc_final: 0.7576 (t-90)
REVERT: C  233 LYS cc_start: 0.9025 (tptt) cc_final: 0.8763 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2177
  time to fit residues: 41.6366
Evaluate side-chains
  89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 55 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.092464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070189 restraints weight = 26764.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.070085 restraints weight = 18386.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.070588 restraints weight = 16066.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7246  Z= 0.139
  Angle     :  0.615   7.352   9799  Z= 0.317
  Chirality :  0.042   0.145   1064
  Planarity :  0.004   0.075   1229
  Dihedral  :  4.760  20.746    928
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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: -0.28 (0.30), residues: 850
  helix:  1.26 (0.29), residues: 291
  sheet: -0.39 (0.30), residues: 297
  loop : -1.48 (0.43), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 232 
 HIS   0.004   0.001   HIS C 190 
 PHE   0.033   0.001   PHE C 325 
 TYR   0.018   0.001   TYR C 203 
 ARG   0.008   0.000   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  357)
  hydrogen bonds       : angle       4.93597 ( 1062)
  SS BOND              : bond        0.00470 (    3)
  SS BOND              : angle       1.01489 (    6)
  covalent geometry    : bond        0.00303 ( 7243)
  covalent geometry    : angle       0.61443 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9125 (tmm) cc_final: 0.8875 (tmm)
REVERT: B  222 MET cc_start: 0.7893 (tmm) cc_final: 0.7606 (tmm)
REVERT: B  309 ILE cc_start: 0.9565 (tp) cc_final: 0.9342 (pt)
REVERT: B  333 MET cc_start: 0.6915 (tpp) cc_final: 0.6358 (tmm)
REVERT: C   79 MET cc_start: 0.8921 (mmp) cc_final: 0.8463 (mmm)
REVERT: C  202 ASP cc_start: 0.7890 (t0) cc_final: 0.7667 (t0)
REVERT: C  233 LYS cc_start: 0.8867 (tptt) cc_final: 0.8582 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.3104
  time to fit residues: 49.6061
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0020
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.7994

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.092775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.066734 restraints weight = 27048.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068361 restraints weight = 16832.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069479 restraints weight = 12486.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7246  Z= 0.121
  Angle     :  0.586   8.840   9799  Z= 0.300
  Chirality :  0.042   0.160   1064
  Planarity :  0.005   0.113   1229
  Dihedral  :  4.625  20.982    928
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  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: -0.13 (0.30), residues: 850
  helix:  1.37 (0.29), residues: 290
  sheet: -0.24 (0.30), residues: 296
  loop : -1.45 (0.42), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 232 
 HIS   0.003   0.001   HIS B 132 
 PHE   0.016   0.001   PHE C 325 
 TYR   0.016   0.001   TYR C 203 
 ARG   0.025   0.001   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  357)
  hydrogen bonds       : angle       4.66250 ( 1062)
  SS BOND              : bond        0.00549 (    3)
  SS BOND              : angle       1.18335 (    6)
  covalent geometry    : bond        0.00265 ( 7243)
  covalent geometry    : angle       0.58579 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9183 (tmm) cc_final: 0.8943 (tmm)
REVERT: B  222 MET cc_start: 0.7931 (tmm) cc_final: 0.7646 (tmm)
REVERT: B  309 ILE cc_start: 0.9522 (tp) cc_final: 0.9295 (pt)
REVERT: B  333 MET cc_start: 0.6792 (tpp) cc_final: 0.6384 (tmm)
REVERT: C   79 MET cc_start: 0.8843 (mmp) cc_final: 0.8424 (mmm)
REVERT: C  222 MET cc_start: 0.8457 (ppp) cc_final: 0.8256 (ppp)
REVERT: C  233 LYS cc_start: 0.8982 (tptt) cc_final: 0.8707 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2407
  time to fit residues: 41.4813
Evaluate side-chains
  89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0170
   chunk 57 optimal weight:   20.0000
   overall best weight:    0.7624

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.092742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070308 restraints weight = 26590.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070382 restraints weight = 19390.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.070951 restraints weight = 15219.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7246  Z= 0.117
  Angle     :  0.590   7.622   9799  Z= 0.301
  Chirality :  0.042   0.162   1064
  Planarity :  0.005   0.101   1229
  Dihedral  :  4.529  21.142    928
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.05 (0.30), residues: 850
  helix:  1.44 (0.29), residues: 290
  sheet: -0.17 (0.30), residues: 296
  loop : -1.44 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 232 
 HIS   0.012   0.001   HIS C 132 
 PHE   0.014   0.001   PHE A 320 
 TYR   0.015   0.001   TYR C 203 
 ARG   0.011   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  357)
  hydrogen bonds       : angle       4.55593 ( 1062)
  SS BOND              : bond        0.00080 (    3)
  SS BOND              : angle       1.29395 (    6)
  covalent geometry    : bond        0.00257 ( 7243)
  covalent geometry    : angle       0.58969 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9159 (tmm) cc_final: 0.8893 (tmm)
REVERT: B  222 MET cc_start: 0.7803 (tmm) cc_final: 0.7535 (tmm)
REVERT: B  268 ASN cc_start: 0.8893 (t0) cc_final: 0.8617 (t0)
REVERT: B  295 GLN cc_start: 0.8989 (mt0) cc_final: 0.8771 (tt0)
REVERT: B  333 MET cc_start: 0.7112 (tpp) cc_final: 0.6661 (tmm)
REVERT: C   79 MET cc_start: 0.8860 (mmp) cc_final: 0.8419 (mmm)
REVERT: C  202 ASP cc_start: 0.7843 (t0) cc_final: 0.7631 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1956
  time to fit residues: 32.4339
Evaluate side-chains
  86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0030
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0270
   chunk 69 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.3848

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

Flipped N/Q/H residues before XYZ refinement:
** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.093865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.070066 restraints weight = 26736.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.070481 restraints weight = 18479.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.070965 restraints weight = 14856.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7246  Z= 0.104
  Angle     :  0.576   7.496   9799  Z= 0.292
  Chirality :  0.042   0.157   1064
  Planarity :  0.004   0.086   1229
  Dihedral  :  4.336  21.409    928
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.02 (0.30), residues: 850
  helix:  1.48 (0.29), residues: 289
  sheet: -0.04 (0.31), residues: 288
  loop : -1.47 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 232 
 HIS   0.011   0.001   HIS C 132 
 PHE   0.023   0.001   PHE A 316 
 TYR   0.013   0.001   TYR C 203 
 ARG   0.008   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  357)
  hydrogen bonds       : angle       4.34213 ( 1062)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       1.03382 (    6)
  covalent geometry    : bond        0.00226 ( 7243)
  covalent geometry    : angle       0.57577 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9156 (tmm) cc_final: 0.8854 (tmm)
REVERT: B  232 TRP cc_start: 0.7884 (m-10) cc_final: 0.7676 (m-10)
REVERT: B  268 ASN cc_start: 0.8912 (t0) cc_final: 0.8571 (t0)
REVERT: B  295 GLN cc_start: 0.8987 (mt0) cc_final: 0.8783 (tt0)
REVERT: B  333 MET cc_start: 0.7023 (tpp) cc_final: 0.6499 (tmm)
REVERT: C   79 MET cc_start: 0.8848 (mmp) cc_final: 0.8402 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1994
  time to fit residues: 32.5964
Evaluate side-chains
  90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.091176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.065124 restraints weight = 26637.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.066755 restraints weight = 16523.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067879 restraints weight = 12209.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7246  Z= 0.158
  Angle     :  0.610   8.471   9799  Z= 0.312
  Chirality :  0.042   0.251   1064
  Planarity :  0.005   0.111   1229
  Dihedral  :  4.583  24.145    928
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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:  0.06 (0.30), residues: 850
  helix:  1.56 (0.29), residues: 286
  sheet: -0.18 (0.31), residues: 293
  loop : -1.26 (0.42), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 232 
 HIS   0.009   0.001   HIS C 132 
 PHE   0.026   0.002   PHE A 316 
 TYR   0.025   0.002   TYR B  75 
 ARG   0.011   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  357)
  hydrogen bonds       : angle       4.48090 ( 1062)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       1.67127 (    6)
  covalent geometry    : bond        0.00354 ( 7243)
  covalent geometry    : angle       0.60887 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.9406 (m-80) cc_final: 0.9175 (m-80)
REVERT: B  295 GLN cc_start: 0.9095 (mt0) cc_final: 0.8759 (tt0)
REVERT: B  333 MET cc_start: 0.6884 (tpp) cc_final: 0.6490 (tmm)
REVERT: C   79 MET cc_start: 0.8862 (mmp) cc_final: 0.8468 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1546
  time to fit residues: 24.5211
Evaluate side-chains
  90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
C 136 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.091184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.065075 restraints weight = 27159.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.066711 restraints weight = 16837.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.067821 restraints weight = 12395.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7246  Z= 0.133
  Angle     :  0.613   7.658   9799  Z= 0.309
  Chirality :  0.042   0.222   1064
  Planarity :  0.005   0.099   1229
  Dihedral  :  4.528  25.675    928
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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:  0.09 (0.30), residues: 850
  helix:  1.64 (0.29), residues: 286
  sheet: -0.18 (0.31), residues: 292
  loop : -1.30 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 232 
 HIS   0.008   0.001   HIS C 132 
 PHE   0.027   0.001   PHE A 316 
 TYR   0.019   0.001   TYR B  75 
 ARG   0.010   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  357)
  hydrogen bonds       : angle       4.43633 ( 1062)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       1.44131 (    6)
  covalent geometry    : bond        0.00301 ( 7243)
  covalent geometry    : angle       0.61236 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 MET cc_start: 0.8927 (tpp) cc_final: 0.8612 (tpp)
REVERT: A  316 PHE cc_start: 0.9378 (m-80) cc_final: 0.9153 (m-80)
REVERT: B  232 TRP cc_start: 0.8056 (m-10) cc_final: 0.7813 (m-10)
REVERT: B  268 ASN cc_start: 0.8929 (t0) cc_final: 0.8608 (t0)
REVERT: B  295 GLN cc_start: 0.9128 (mt0) cc_final: 0.8801 (mt0)
REVERT: B  333 MET cc_start: 0.6922 (tpp) cc_final: 0.6542 (tmm)
REVERT: C   79 MET cc_start: 0.8865 (mmp) cc_final: 0.8471 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1565
  time to fit residues: 24.5939
Evaluate side-chains
  89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.090696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.064666 restraints weight = 27336.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.066282 restraints weight = 16959.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.067399 restraints weight = 12522.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7246  Z= 0.139
  Angle     :  0.620   7.966   9799  Z= 0.312
  Chirality :  0.042   0.222   1064
  Planarity :  0.005   0.097   1229
  Dihedral  :  4.587  25.175    928
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.30), residues: 850
  helix:  1.67 (0.29), residues: 286
  sheet: -0.18 (0.31), residues: 293
  loop : -1.26 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 232 
 HIS   0.008   0.001   HIS C 132 
 PHE   0.025   0.001   PHE A 316 
 TYR   0.018   0.001   TYR C 203 
 ARG   0.009   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  357)
  hydrogen bonds       : angle       4.46731 ( 1062)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       1.36284 (    6)
  covalent geometry    : bond        0.00316 ( 7243)
  covalent geometry    : angle       0.61884 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.9409 (m-80) cc_final: 0.9158 (m-80)
REVERT: B  232 TRP cc_start: 0.8094 (m-10) cc_final: 0.7856 (m-10)
REVERT: B  295 GLN cc_start: 0.9135 (mt0) cc_final: 0.8805 (mt0)
REVERT: B  316 PHE cc_start: 0.9282 (t80) cc_final: 0.8953 (t80)
REVERT: B  333 MET cc_start: 0.6875 (tpp) cc_final: 0.6497 (tmm)
REVERT: C   79 MET cc_start: 0.8855 (mmp) cc_final: 0.8374 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1574
  time to fit residues: 23.5259
Evaluate side-chains
  88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0980
   chunk 62 optimal weight:    8.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.091980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069276 restraints weight = 27525.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.069474 restraints weight = 19556.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.069834 restraints weight = 15937.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7246  Z= 0.117
  Angle     :  0.632   8.482   9799  Z= 0.313
  Chirality :  0.043   0.219   1064
  Planarity :  0.004   0.091   1229
  Dihedral  :  4.545  24.625    928
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.16 (0.30), residues: 850
  helix:  1.69 (0.29), residues: 286
  sheet: -0.11 (0.31), residues: 294
  loop : -1.30 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 133 
 HIS   0.008   0.001   HIS C 132 
 PHE   0.025   0.001   PHE A 316 
 TYR   0.017   0.001   TYR B 158 
 ARG   0.009   0.000   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  357)
  hydrogen bonds       : angle       4.40905 ( 1062)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       1.27341 (    6)
  covalent geometry    : bond        0.00264 ( 7243)
  covalent geometry    : angle       0.63151 ( 9793)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.9328 (m-80) cc_final: 0.9090 (m-80)
REVERT: B  295 GLN cc_start: 0.9124 (mt0) cc_final: 0.8831 (mt0)
REVERT: B  316 PHE cc_start: 0.9096 (t80) cc_final: 0.8793 (t80)
REVERT: B  333 MET cc_start: 0.7142 (tpp) cc_final: 0.6634 (tmm)
REVERT: C   79 MET cc_start: 0.8862 (mmp) cc_final: 0.8468 (mmm)
REVERT: C  291 ASP cc_start: 0.7894 (t70) cc_final: 0.7672 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1565
  time to fit residues: 25.6049
Evaluate side-chains
  88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.090237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064385 restraints weight = 27040.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065969 restraints weight = 16753.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.067078 restraints weight = 12370.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7246  Z= 0.166
  Angle     :  0.641   8.324   9799  Z= 0.327
  Chirality :  0.042   0.214   1064
  Planarity :  0.005   0.108   1229
  Dihedral  :  4.715  25.712    928
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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:  0.07 (0.30), residues: 850
  helix:  1.65 (0.29), residues: 286
  sheet: -0.22 (0.30), residues: 295
  loop : -1.31 (0.41), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 232 
 HIS   0.008   0.001   HIS C 132 
 PHE   0.024   0.002   PHE A 316 
 TYR   0.022   0.002   TYR C 203 
 ARG   0.011   0.001   ARG B 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  357)
  hydrogen bonds       : angle       4.59741 ( 1062)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       1.41813 (    6)
  covalent geometry    : bond        0.00375 ( 7243)
  covalent geometry    : angle       0.63979 ( 9793)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2898.51 seconds
wall clock time: 53 minutes 42.49 seconds (3222.49 seconds total)