Starting phenix.real_space_refine
on Fri Aug 22 19:16:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/08_2025/8h8d_34543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/08_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_34543/08_2025/8h8d_34543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2025/8h8d_34543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2025/8h8d_34543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/08_2025/8h8d_34543.cif"
  }
  resolution = 4.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.09, per 1000 atoms: 0.30
  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: 0.67
  Conformation dependent library (CDL) restraints added in 449.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.23
  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: 1.16

  Time building geometry restraints manager: 0.77 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:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.210
-------------------------------------------------------------------------------
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 : 18.75
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (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
 ARG   0.003   0.000   ARG C 181 
 TYR   0.014   0.001   TYR A 120 
 PHE   0.022   0.001   PHE A 320 
 TRP   0.035   0.002   TRP C 133 
 HIS   0.007   0.001   HIS C 132 

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

*********************** 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  : 0.327 
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: 0.0897
  time to fit residues: 15.5996
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  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.091860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.065284 restraints weight = 26872.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.066983 restraints weight = 16461.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.068046 restraints weight = 12090.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.068786 restraints weight = 9942.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069114 restraints weight = 8791.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7246  Z= 0.181
  Angle     :  0.658   8.349   9799  Z= 0.347
  Chirality :  0.044   0.186   1064
  Planarity :  0.005   0.072   1229
  Dihedral  :  4.881  20.041    928
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.30), residues: 850
  helix:  1.34 (0.29), residues: 293
  sheet: -0.45 (0.30), residues: 295
  loop : -1.44 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG B 337 
 TYR   0.019   0.002   TYR B 158 
 PHE   0.025   0.002   PHE A 320 
 TRP   0.013   0.002   TRP B 232 
 HIS   0.006   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7243)
  covalent geometry    : angle       0.65680 ( 9793)
  SS BOND              : bond        0.01418 (    3)
  SS BOND              : angle       1.99998 (    6)
  hydrogen bonds       : bond        0.04821 (  357)
  hydrogen bonds       : angle       5.44813 ( 1062)

*********************** 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
  136 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 MET cc_start: 0.8724 (ptm) cc_final: 0.8470 (ppp)
REVERT: B  158 TYR cc_start: 0.8045 (m-10) cc_final: 0.7778 (m-10)
REVERT: B  333 MET cc_start: 0.6792 (tpp) cc_final: 0.6307 (tmm)
REVERT: C   79 MET cc_start: 0.8809 (mmp) cc_final: 0.8517 (mmm)
REVERT: C  222 MET cc_start: 0.8567 (ppp) cc_final: 0.8333 (ppp)
REVERT: C  233 LYS cc_start: 0.9068 (tptt) cc_final: 0.8796 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0800
  time to fit residues: 15.0517
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  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0970
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   chunk 43 optimal weight:    0.0570
   overall best weight:    0.4296

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.093038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070680 restraints weight = 26792.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.070485 restraints weight = 18471.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.071237 restraints weight = 16028.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.071419 restraints weight = 12700.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.071735 restraints weight = 11715.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7246  Z= 0.123
  Angle     :  0.610   7.453   9799  Z= 0.314
  Chirality :  0.042   0.146   1064
  Planarity :  0.004   0.076   1229
  Dihedral  :  4.669  20.778    928
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.30), residues: 850
  helix:  1.27 (0.29), residues: 293
  sheet: -0.33 (0.30), residues: 292
  loop : -1.42 (0.43), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 181 
 TYR   0.014   0.001   TYR C 203 
 PHE   0.028   0.001   PHE C 325 
 TRP   0.013   0.001   TRP C 241 
 HIS   0.004   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7243)
  covalent geometry    : angle       0.61017 ( 9793)
  SS BOND              : bond        0.00090 (    3)
  SS BOND              : angle       0.87220 (    6)
  hydrogen bonds       : bond        0.04075 (  357)
  hydrogen bonds       : angle       4.94744 ( 1062)

*********************** 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
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9135 (tmm) cc_final: 0.8885 (tmm)
REVERT: B  222 MET cc_start: 0.7887 (tmm) cc_final: 0.7629 (tmm)
REVERT: B  309 ILE cc_start: 0.9581 (tp) cc_final: 0.9328 (pt)
REVERT: B  333 MET cc_start: 0.6970 (tpp) cc_final: 0.6432 (tmm)
REVERT: C   79 MET cc_start: 0.8910 (mmp) cc_final: 0.8465 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0733
  time to fit residues: 12.4458
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  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0000
   chunk 2 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.092857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.069578 restraints weight = 27030.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.070058 restraints weight = 19399.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.070388 restraints weight = 14274.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.070739 restraints weight = 12609.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.071046 restraints weight = 11412.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7246  Z= 0.124
  Angle     :  0.584   8.923   9799  Z= 0.299
  Chirality :  0.041   0.154   1064
  Planarity :  0.005   0.107   1229
  Dihedral  :  4.589  20.707    928
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.30), residues: 850
  helix:  1.39 (0.28), residues: 290
  sheet: -0.24 (0.30), residues: 296
  loop : -1.44 (0.42), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 181 
 TYR   0.015   0.001   TYR C 203 
 PHE   0.015   0.001   PHE A 320 
 TRP   0.017   0.001   TRP B 232 
 HIS   0.003   0.001   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7243)
  covalent geometry    : angle       0.58356 ( 9793)
  SS BOND              : bond        0.01039 (    3)
  SS BOND              : angle       1.17711 (    6)
  hydrogen bonds       : bond        0.03624 (  357)
  hydrogen bonds       : angle       4.67760 ( 1062)

*********************** 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
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8908 (tmm) cc_final: 0.8615 (tmm)
REVERT: A  308 MET cc_start: 0.9110 (tmm) cc_final: 0.8858 (tmm)
REVERT: B  222 MET cc_start: 0.7856 (tmm) cc_final: 0.7608 (tmm)
REVERT: B  309 ILE cc_start: 0.9486 (tp) cc_final: 0.9246 (pt)
REVERT: B  333 MET cc_start: 0.6979 (tpp) cc_final: 0.6553 (tmm)
REVERT: C   79 MET cc_start: 0.8844 (mmp) cc_final: 0.8406 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0653
  time to fit residues: 11.2618
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  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B 295 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.091997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.066183 restraints weight = 27081.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.067863 restraints weight = 16620.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.069006 restraints weight = 12192.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.069730 restraints weight = 9939.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.070246 restraints weight = 8746.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7246  Z= 0.134
  Angle     :  0.594   7.607   9799  Z= 0.304
  Chirality :  0.042   0.154   1064
  Planarity :  0.005   0.115   1229
  Dihedral  :  4.561  20.667    928
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.30), residues: 850
  helix:  1.47 (0.29), residues: 290
  sheet: -0.17 (0.31), residues: 286
  loop : -1.47 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 181 
 TYR   0.018   0.001   TYR C 203 
 PHE   0.014   0.001   PHE A 320 
 TRP   0.019   0.001   TRP B 232 
 HIS   0.013   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7243)
  covalent geometry    : angle       0.59298 ( 9793)
  SS BOND              : bond        0.00089 (    3)
  SS BOND              : angle       1.17977 (    6)
  hydrogen bonds       : bond        0.03527 (  357)
  hydrogen bonds       : angle       4.59963 ( 1062)

*********************** 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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.197 
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  111 MET cc_start: 0.8903 (tmm) cc_final: 0.8566 (tmm)
REVERT: A  308 MET cc_start: 0.9215 (tmm) cc_final: 0.8974 (tmm)
REVERT: B  222 MET cc_start: 0.7869 (tmm) cc_final: 0.7602 (tmm)
REVERT: B  333 MET cc_start: 0.6923 (tpp) cc_final: 0.6527 (tmm)
REVERT: C   79 MET cc_start: 0.8849 (mmp) cc_final: 0.8435 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0511
  time to fit residues: 8.3698
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  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.092712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.066589 restraints weight = 26965.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068263 restraints weight = 16573.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069392 restraints weight = 12167.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.069977 restraints weight = 9964.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.070568 restraints weight = 8883.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7246  Z= 0.112
  Angle     :  0.575   7.418   9799  Z= 0.293
  Chirality :  0.041   0.147   1064
  Planarity :  0.004   0.094   1229
  Dihedral  :  4.412  20.386    928
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.30), residues: 850
  helix:  1.46 (0.29), residues: 291
  sheet: -0.11 (0.31), residues: 286
  loop : -1.47 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 181 
 TYR   0.015   0.001   TYR B 158 
 PHE   0.023   0.001   PHE A 316 
 TRP   0.017   0.001   TRP B 232 
 HIS   0.007   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7243)
  covalent geometry    : angle       0.57504 ( 9793)
  SS BOND              : bond        0.00071 (    3)
  SS BOND              : angle       0.88225 (    6)
  hydrogen bonds       : bond        0.03291 (  357)
  hydrogen bonds       : angle       4.42423 ( 1062)

*********************** 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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8868 (tmm) cc_final: 0.8531 (tmm)
REVERT: A  308 MET cc_start: 0.9117 (tmm) cc_final: 0.8826 (tmm)
REVERT: B  268 ASN cc_start: 0.8867 (t0) cc_final: 0.8606 (t0)
REVERT: B  333 MET cc_start: 0.6906 (tpp) cc_final: 0.6506 (tmm)
REVERT: C   79 MET cc_start: 0.8828 (mmp) cc_final: 0.8373 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0696
  time to fit residues: 11.0911
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  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   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 = 0.3715 r_free = 0.3715 target = 0.092896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.066368 restraints weight = 26973.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.068096 restraints weight = 16812.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.069242 restraints weight = 12349.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.069829 restraints weight = 10118.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.070379 restraints weight = 9021.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.4069

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= 0.115
  Angle     :  0.593   8.168   9799  Z= 0.299
  Chirality :  0.043   0.252   1064
  Planarity :  0.004   0.093   1229
  Dihedral  :  4.430  20.238    928
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.30), residues: 850
  helix:  1.48 (0.29), residues: 291
  sheet: -0.08 (0.31), residues: 287
  loop : -1.39 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.025   0.001   TYR B  75 
 PHE   0.031   0.001   PHE A 316 
 TRP   0.022   0.001   TRP B 232 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7243)
  covalent geometry    : angle       0.59190 ( 9793)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       1.53610 (    6)
  hydrogen bonds       : bond        0.03242 (  357)
  hydrogen bonds       : angle       4.36026 ( 1062)

*********************** 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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8877 (tmm) cc_final: 0.8487 (tmm)
REVERT: A  316 PHE cc_start: 0.9403 (m-80) cc_final: 0.9175 (m-80)
REVERT: B  268 ASN cc_start: 0.8897 (t0) cc_final: 0.8611 (t0)
REVERT: B  333 MET cc_start: 0.6863 (tpp) cc_final: 0.6470 (tmm)
REVERT: C   79 MET cc_start: 0.8852 (mmp) cc_final: 0.8416 (mmm)
REVERT: C  222 MET cc_start: 0.8471 (ppp) cc_final: 0.8257 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0580
  time to fit residues: 9.5507
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  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0020
   chunk 75 optimal weight:    0.0370
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5668

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.093226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.069053 restraints weight = 27177.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.069733 restraints weight = 19402.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.069995 restraints weight = 14848.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.070645 restraints weight = 13033.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070738 restraints weight = 11605.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7246  Z= 0.107
  Angle     :  0.594   7.663   9799  Z= 0.299
  Chirality :  0.042   0.225   1064
  Planarity :  0.004   0.078   1229
  Dihedral  :  4.331  23.677    928
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.72
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.30), residues: 850
  helix:  1.44 (0.29), residues: 291
  sheet: -0.05 (0.31), residues: 286
  loop : -1.40 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 181 
 TYR   0.021   0.001   TYR B  75 
 PHE   0.026   0.001   PHE A 316 
 TRP   0.019   0.001   TRP B 232 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7243)
  covalent geometry    : angle       0.59348 ( 9793)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       1.25932 (    6)
  hydrogen bonds       : bond        0.03155 (  357)
  hydrogen bonds       : angle       4.27484 ( 1062)

*********************** 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
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8927 (tmm) cc_final: 0.8501 (tmm)
REVERT: B  232 TRP cc_start: 0.7654 (m-10) cc_final: 0.6906 (m-10)
REVERT: B  268 ASN cc_start: 0.8918 (t0) cc_final: 0.8608 (t0)
REVERT: B  333 MET cc_start: 0.7047 (tpp) cc_final: 0.6621 (tmm)
REVERT: C   79 MET cc_start: 0.8854 (mmp) cc_final: 0.8411 (mmm)
REVERT: C  222 MET cc_start: 0.8487 (ppp) cc_final: 0.8273 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0600
  time to fit residues: 9.7823
Evaluate side-chains
  94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0570
   chunk 27 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7906

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.092989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.066201 restraints weight = 27167.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.067899 restraints weight = 17101.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.068978 restraints weight = 12688.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.069767 restraints weight = 10467.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.070155 restraints weight = 9213.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4325

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= 0.114
  Angle     :  0.600   8.093   9799  Z= 0.300
  Chirality :  0.042   0.220   1064
  Planarity :  0.004   0.079   1229
  Dihedral  :  4.328  22.624    928
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.30), residues: 850
  helix:  1.51 (0.29), residues: 291
  sheet: -0.02 (0.31), residues: 292
  loop : -1.39 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 181 
 TYR   0.014   0.001   TYR C 203 
 PHE   0.021   0.001   PHE B 316 
 TRP   0.018   0.001   TRP B 232 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7243)
  covalent geometry    : angle       0.59971 ( 9793)
  SS BOND              : bond        0.00116 (    3)
  SS BOND              : angle       1.23054 (    6)
  hydrogen bonds       : bond        0.03135 (  357)
  hydrogen bonds       : angle       4.29707 ( 1062)

*********************** 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
  110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.9270 (m-10) cc_final: 0.9037 (m-80)
REVERT: B  111 MET cc_start: 0.7936 (tmm) cc_final: 0.7605 (tmm)
REVERT: B  232 TRP cc_start: 0.7654 (m-10) cc_final: 0.7253 (m-10)
REVERT: B  333 MET cc_start: 0.6917 (tpp) cc_final: 0.6540 (tmm)
REVERT: C   79 MET cc_start: 0.8847 (mmp) cc_final: 0.8421 (mmm)
REVERT: C  222 MET cc_start: 0.8478 (ppp) cc_final: 0.8244 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0611
  time to fit residues: 9.8943
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  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 54 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0980
   chunk 65 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0020
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.2966

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.094194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.070767 restraints weight = 27077.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.070839 restraints weight = 21348.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.071241 restraints weight = 15938.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.071717 restraints weight = 14319.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.071876 restraints weight = 12950.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7246  Z= 0.107
  Angle     :  0.611   8.486   9799  Z= 0.302
  Chirality :  0.043   0.219   1064
  Planarity :  0.004   0.070   1229
  Dihedral  :  4.255  22.870    928
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 850
  helix:  1.53 (0.29), residues: 291
  sheet: -0.05 (0.31), residues: 291
  loop : -1.28 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 181 
 TYR   0.014   0.001   TYR B 158 
 PHE   0.014   0.001   PHE C 325 
 TRP   0.022   0.001   TRP C 306 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7243)
  covalent geometry    : angle       0.61072 ( 9793)
  SS BOND              : bond        0.00090 (    3)
  SS BOND              : angle       1.02134 (    6)
  hydrogen bonds       : bond        0.03079 (  357)
  hydrogen bonds       : angle       4.23921 ( 1062)

********************** 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  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 PHE cc_start: 0.9168 (m-10) cc_final: 0.8963 (m-80)
REVERT: B  232 TRP cc_start: 0.7506 (m-10) cc_final: 0.6767 (m-10)
REVERT: B  268 ASN cc_start: 0.8891 (t0) cc_final: 0.8555 (t0)
REVERT: B  333 MET cc_start: 0.7160 (tpp) cc_final: 0.6670 (tmm)
REVERT: C   79 MET cc_start: 0.8862 (mmp) cc_final: 0.8437 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0611
  time to fit residues: 10.1924
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  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.089941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.066407 restraints weight = 27229.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.067214 restraints weight = 19527.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.067480 restraints weight = 14115.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.067897 restraints weight = 12814.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.068061 restraints weight = 11521.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7246  Z= 0.213
  Angle     :  0.653   8.359   9799  Z= 0.335
  Chirality :  0.042   0.222   1064
  Planarity :  0.005   0.116   1229
  Dihedral  :  4.734  25.637    928
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.30), residues: 850
  helix:  1.57 (0.29), residues: 290
  sheet: -0.23 (0.31), residues: 297
  loop : -1.52 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 181 
 TYR   0.023   0.002   TYR C 203 
 PHE   0.020   0.002   PHE C 234 
 TRP   0.032   0.002   TRP B 232 
 HIS   0.006   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 7243)
  covalent geometry    : angle       0.65217 ( 9793)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       1.45890 (    6)
  hydrogen bonds       : bond        0.03435 (  357)
  hydrogen bonds       : angle       4.58458 ( 1062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1301.14 seconds
wall clock time: 23 minutes 11.15 seconds (1391.15 seconds total)