Starting phenix.real_space_refine
on Tue Feb  3 21:21:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8d_34543/02_2026/8h8d_34543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8d_34543/02_2026/8h8d_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_34543/02_2026/8h8d_34543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8d_34543/02_2026/8h8d_34543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8d_34543/02_2026/8h8d_34543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8d_34543/02_2026/8h8d_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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: 1.32, per 1000 atoms: 0.19
  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: 0.48
  Conformation dependent library (CDL) restraints added in 189.5 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: 0.22
  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: 0.90

  Time building geometry restraints manager: 0.62 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:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.600
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.250
-------------------------------------------------------------------------------
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 are 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  : 0.278 
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: 0.0750
  time to fit residues: 13.1738
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  : 0.254 
-------------------------------------------------------------------------------
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 are 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  : 0.291 
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  169 HIS cc_start: 0.7707 (t-170) cc_final: 0.7507 (t-90)
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: 0.0655
  time to fit residues: 12.4666
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  : 0.174 
-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.093114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.070622 restraints weight = 26695.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.070479 restraints weight = 18525.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.071025 restraints weight = 15931.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.071354 restraints weight = 12909.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.071614 restraints weight = 11808.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3173

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= 0.120
  Angle     :  0.612   7.501   9799  Z= 0.314
  Chirality :  0.042   0.147   1064
  Planarity :  0.004   0.074   1229
  Dihedral  :  4.675  20.814    928
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  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 are not related in a simple way.
  whole: -0.23 (0.30), residues: 850
  helix:  1.26 (0.29), residues: 293
  sheet: -0.33 (0.30), residues: 292
  loop : -1.43 (0.43), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 181 
 TYR   0.015   0.001   TYR C 203 
 PHE   0.026   0.001   PHE C 325 
 TRP   0.013   0.001   TRP C 241 
 HIS   0.005   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7243)
  covalent geometry    : angle       0.61171 ( 9793)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       0.81986 (    6)
  hydrogen bonds       : bond        0.04066 (  357)
  hydrogen bonds       : angle       4.92631 ( 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
  118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm)
REVERT: B  222 MET cc_start: 0.7891 (tmm) cc_final: 0.7617 (tmm)
REVERT: B  309 ILE cc_start: 0.9584 (tp) cc_final: 0.9335 (pt)
REVERT: B  333 MET cc_start: 0.6961 (tpp) cc_final: 0.6421 (tmm)
REVERT: C   79 MET cc_start: 0.8907 (mmp) cc_final: 0.8465 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0552
  time to fit residues: 9.4031
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  : 0.262 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.090970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.067549 restraints weight = 27229.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.067969 restraints weight = 20138.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.068322 restraints weight = 14625.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.068628 restraints weight = 12980.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.068992 restraints weight = 11785.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7246  Z= 0.158
  Angle     :  0.601   9.470   9799  Z= 0.311
  Chirality :  0.041   0.158   1064
  Planarity :  0.005   0.126   1229
  Dihedral  :  4.703  19.596    928
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.30), residues: 850
  helix:  1.42 (0.28), residues: 290
  sheet: -0.22 (0.31), residues: 286
  loop : -1.53 (0.42), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG B 181 
 TYR   0.019   0.001   TYR C 203 
 PHE   0.019   0.002   PHE A 320 
 TRP   0.022   0.002   TRP B 232 
 HIS   0.005   0.001   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7243)
  covalent geometry    : angle       0.60069 ( 9793)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       1.38156 (    6)
  hydrogen bonds       : bond        0.03685 (  357)
  hydrogen bonds       : angle       4.77006 ( 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
  113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9136 (tmm) cc_final: 0.8870 (tmm)
REVERT: B  222 MET cc_start: 0.7906 (tmm) cc_final: 0.7620 (tmm)
REVERT: B  309 ILE cc_start: 0.9504 (tp) cc_final: 0.9264 (pt)
REVERT: B  333 MET cc_start: 0.6980 (tpp) cc_final: 0.6549 (tmm)
REVERT: C   79 MET cc_start: 0.8899 (mmp) cc_final: 0.8434 (mmm)
REVERT: C  222 MET cc_start: 0.8473 (ppp) cc_final: 0.8256 (ppp)
REVERT: C  321 LYS cc_start: 0.9581 (tptt) cc_final: 0.9219 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0557
  time to fit residues: 9.0062
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  : 0.291 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0170
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0370
   chunk 26 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.6102

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
B 295 GLN
C 149 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.090429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.067152 restraints weight = 27250.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.067754 restraints weight = 20347.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.068085 restraints weight = 14338.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.068423 restraints weight = 12899.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.068677 restraints weight = 11671.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7246  Z= 0.160
  Angle     :  0.611   7.695   9799  Z= 0.317
  Chirality :  0.042   0.157   1064
  Planarity :  0.005   0.127   1229
  Dihedral  :  4.745  20.010    928
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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 are not related in a simple way.
  whole: -0.08 (0.30), residues: 850
  helix:  1.46 (0.28), residues: 290
  sheet: -0.19 (0.31), residues: 292
  loop : -1.51 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 181 
 TYR   0.021   0.001   TYR C 203 
 PHE   0.017   0.002   PHE C 325 
 TRP   0.024   0.002   TRP B 232 
 HIS   0.014   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7243)
  covalent geometry    : angle       0.61047 ( 9793)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       1.39891 (    6)
  hydrogen bonds       : bond        0.03613 (  357)
  hydrogen bonds       : angle       4.70912 ( 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
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.161 
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: 0.9147 (tmm) cc_final: 0.8869 (tmm)
REVERT: B  222 MET cc_start: 0.7967 (tmm) cc_final: 0.7707 (tmm)
REVERT: B  333 MET cc_start: 0.7038 (tpp) cc_final: 0.6608 (tmm)
REVERT: C   79 MET cc_start: 0.8879 (mmp) cc_final: 0.8412 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0544
  time to fit residues: 8.1221
Evaluate side-chains
  85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.2188

-------------------------------------------------------------------------------
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 = 0.090793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.064154 restraints weight = 27296.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.065801 restraints weight = 16802.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.066910 restraints weight = 12368.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.067618 restraints weight = 10147.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.068152 restraints weight = 8950.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.3839

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= 0.135
  Angle     :  0.588   7.449   9799  Z= 0.303
  Chirality :  0.041   0.165   1064
  Planarity :  0.005   0.110   1229
  Dihedral  :  4.600  20.221    928
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  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 are not related in a simple way.
  whole:  0.00 (0.30), residues: 850
  helix:  1.59 (0.29), residues: 287
  sheet: -0.19 (0.31), residues: 291
  loop : -1.42 (0.41), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 181 
 TYR   0.018   0.001   TYR C 203 
 PHE   0.021   0.001   PHE B 316 
 TRP   0.020   0.001   TRP B 232 
 HIS   0.012   0.001   HIS C 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7243)
  covalent geometry    : angle       0.58728 ( 9793)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       1.11440 (    6)
  hydrogen bonds       : bond        0.03386 (  357)
  hydrogen bonds       : angle       4.57020 ( 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
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9155 (tmm) cc_final: 0.8872 (tmm)
REVERT: A  316 PHE cc_start: 0.9353 (m-10) cc_final: 0.9138 (m-80)
REVERT: B  222 MET cc_start: 0.7846 (tmm) cc_final: 0.7594 (tmm)
REVERT: B  268 ASN cc_start: 0.8919 (t0) cc_final: 0.8605 (t0)
REVERT: B  333 MET cc_start: 0.6849 (tpp) cc_final: 0.6462 (tmm)
REVERT: C   79 MET cc_start: 0.8869 (mmp) cc_final: 0.8383 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0567
  time to fit residues: 8.3696
Evaluate side-chains
  87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 56.2893 > 50:
  distance: 18 - 23:   5.816
  distance: 24 - 25:   5.814
  distance: 24 - 27:   3.513
  distance: 25 - 26:  21.165
  distance: 25 - 31:   9.357
  distance: 27 - 28:   7.106
  distance: 28 - 29:  10.205
  distance: 28 - 30:  12.772
  distance: 32 - 33:   6.153
  distance: 32 - 35:  10.311
  distance: 33 - 34:  14.999
  distance: 33 - 41:  10.636
  distance: 35 - 36:   6.301
  distance: 36 - 37:   3.226
  distance: 36 - 38:  11.092
  distance: 37 - 39:   3.661
  distance: 38 - 40:   3.865
  distance: 39 - 40:   8.935
  distance: 41 - 42:   5.001
  distance: 42 - 43:   4.542
  distance: 42 - 45:  10.045
  distance: 43 - 44:  16.611
  distance: 43 - 49:   5.850
  distance: 45 - 46:  12.599
  distance: 45 - 47:  10.222
  distance: 46 - 48:   7.503
  distance: 49 - 50:  16.078
  distance: 49 - 55:   9.284
  distance: 50 - 51:  22.521
  distance: 50 - 53:  10.493
  distance: 51 - 52:  22.823
  distance: 51 - 56:  16.710
  distance: 53 - 54:  10.597
  distance: 54 - 55:  15.004
  distance: 56 - 57:   4.776
  distance: 56 - 62:  10.802
  distance: 57 - 58:   8.847
  distance: 57 - 60:   7.400
  distance: 58 - 59:   5.873
  distance: 58 - 63:   8.794
  distance: 60 - 61:  11.195
  distance: 61 - 62:  14.088
  distance: 63 - 64:   9.002
  distance: 64 - 65:   3.706
  distance: 64 - 67:  13.840
  distance: 65 - 66:   7.920
  distance: 65 - 71:  18.588
  distance: 67 - 68:   4.934
  distance: 68 - 69:  14.869
  distance: 68 - 70:  14.906
  distance: 71 - 72:   6.069
  distance: 72 - 73:   8.947
  distance: 72 - 75:   7.450
  distance: 73 - 74:   7.597
  distance: 73 - 80:   4.538
  distance: 75 - 76:   4.471
  distance: 76 - 77:  10.660
  distance: 77 - 78:   9.975
  distance: 78 - 79:  12.284
  distance: 80 - 81:   5.083
  distance: 81 - 82:   4.083
  distance: 82 - 83:   4.125
  distance: 82 - 88:   4.243
  distance: 85 - 86:   6.894
  distance: 85 - 87:  18.585
  distance: 88 - 89:   6.544
  distance: 88 - 94:   8.536
  distance: 89 - 90:  24.720
  distance: 89 - 92:  19.812
  distance: 90 - 91:  35.782
  distance: 90 - 95:   8.122
  distance: 92 - 93:  10.371
  distance: 93 - 94:  20.385
  distance: 95 - 96:  11.869
  distance: 96 - 97:  31.108
  distance: 97 - 98:  26.259
  distance: 97 - 99:   6.792