Starting phenix.real_space_refine
on Tue Mar  3 14:44:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2026/7lf6_23300.map"
  }
  resolution = 3.5
  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=   0.001 sd=   0.022
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      40      5.16       5
     C    4164      2.51       5
     N    1016      2.21       5
     O    1068      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6288
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3144
          Classifications: {'peptide': 407}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.98, per 1000 atoms: 0.31
  Number of scatterers: 6288
  At special positions: 0
  Unit cell: (78.375, 85.8, 81.675, 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      40     16.00
     O    1068      8.00
     N    1016      7.00
     C    4164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 196 " 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: 0.50
  Conformation dependent library (CDL) restraints added in 341.6 milliseconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 50
      removed outlier: 3.718A  pdb=" N   PHE A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 57
      removed outlier: 4.070A  pdb=" N   VAL A  55 " --> pdb=" O   MET A  51 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   HIS A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 102
      removed outlier: 3.631A  pdb=" N   VAL A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 133
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 136 through 164
      removed outlier: 4.436A  pdb=" N   ILE A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 206
      removed outlier: 3.622A  pdb=" N   HIS A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   GLY A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      Proline residue:  A 193  - end of helix
      removed outlier: 3.854A  pdb=" N   PHE A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 223
      removed outlier: 4.486A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   ILE A 218 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 257 through 284
      removed outlier: 4.806A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   ILE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 283 " --> pdb=" O   ASP A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.676A  pdb=" N   PHE A 295 " --> pdb=" O   LYS A 292 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER A 296 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 292 through 296'
    Processing helix  chain 'A' and resid 298 through 333
      removed outlier: 4.412A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      Proline residue:  A 308  - end of helix
      removed outlier: 4.286A  pdb=" N   HIS A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 353
    Processing helix  chain 'A' and resid 354 through 364
      removed outlier: 3.813A  pdb=" N   ALA A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 396
      removed outlier: 3.728A  pdb=" N   GLN A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   MET A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TRP A 394 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 5.617A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 427  - end of helix
    Processing helix  chain 'A' and resid 444 through 469
      Proline residue:  A 456  - end of helix
      removed outlier: 4.787A  pdb=" N   LEU A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LEU A 461 " --> pdb=" O   CYS A 457 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 469 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 50
      removed outlier: 3.719A  pdb=" N   PHE B  39 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 57
      removed outlier: 4.070A  pdb=" N   VAL B  55 " --> pdb=" O   MET B  51 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 102
      removed outlier: 3.631A  pdb=" N   VAL B 101 " --> pdb=" O   ARG B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 133
      Proline residue:  B 124  - end of helix
    Processing helix  chain 'B' and resid 136 through 164
      removed outlier: 4.436A  pdb=" N   ILE B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 206
      removed outlier: 3.622A  pdb=" N   HIS B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   GLY B 192 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      Proline residue:  B 193  - end of helix
      removed outlier: 3.854A  pdb=" N   PHE B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 223
      removed outlier: 4.485A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   ILE B 218 " --> pdb=" O   MET B 214 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 257 through 284
      removed outlier: 4.807A  pdb=" N   LEU B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   ILE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP B 283 " --> pdb=" O   ASP B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.677A  pdb=" N   PHE B 295 " --> pdb=" O   LYS B 292 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B 296 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 292 through 296'
    Processing helix  chain 'B' and resid 298 through 333
      removed outlier: 4.411A  pdb=" N   ALA B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      Proline residue:  B 308  - end of helix
      removed outlier: 4.285A  pdb=" N   HIS B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 353
    Processing helix  chain 'B' and resid 354 through 364
      removed outlier: 3.813A  pdb=" N   ALA B 364 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 396
      removed outlier: 3.727A  pdb=" N   GLN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   MET B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TRP B 394 " --> pdb=" O   GLN B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 415 through 437
      removed outlier: 5.617A  pdb=" N   TYR B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
      Proline residue:  B 427  - end of helix
    Processing helix  chain 'B' and resid 444 through 469
      Proline residue:  B 456  - end of helix
      removed outlier: 4.787A  pdb=" N   LEU B 460 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LEU B 461 " --> pdb=" O   CYS B 457 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA B 469 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1350 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: 0.89

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1932
        1.34 -     1.47: 1612
        1.47 -     1.60: 2836
        1.60 -     1.73: 0
        1.73 -     1.85: 62
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" CB  CYS B 196 "
       pdb=" SG  CYS B 196 "
    ideal  model  delta    sigma   weight residual
    1.808  1.853 -0.045 3.30e-02 9.18e+02 1.86e+00
  bond pdb=" CB  CYS A 196 "
       pdb=" SG  CYS A 196 "
    ideal  model  delta    sigma   weight residual
    1.808  1.852 -0.044 3.30e-02 9.18e+02 1.81e+00
  bond pdb=" CB  MET A 130 "
       pdb=" CG  MET A 130 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" CB  MET B 130 "
       pdb=" CG  MET B 130 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" CB  TRP B 394 "
       pdb=" CG  TRP B 394 "
    ideal  model  delta    sigma   weight residual
    1.498  1.471  0.027 3.10e-02 1.04e+03 7.83e-01
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 8627
        2.22 -     4.45: 129
        4.45 -     6.67: 34
        6.67 -     8.89: 0
        8.89 -    11.12: 2
  Bond angle restraints: 8792
  Sorted by residual:
  angle pdb=" N   ILE B 218 "
        pdb=" CA  ILE B 218 "
        pdb=" C   ILE B 218 "
      ideal   model   delta    sigma   weight residual
     113.42  108.71    4.71 1.17e+00 7.31e-01 1.62e+01
  angle pdb=" N   ILE A 218 "
        pdb=" CA  ILE A 218 "
        pdb=" C   ILE A 218 "
      ideal   model   delta    sigma   weight residual
     113.42  108.73    4.69 1.17e+00 7.31e-01 1.61e+01
  angle pdb=" CB  MET A 130 "
        pdb=" CG  MET A 130 "
        pdb=" SD  MET A 130 "
      ideal   model   delta    sigma   weight residual
     112.70  101.58   11.12 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" CB  MET B 130 "
        pdb=" CG  MET B 130 "
        pdb=" SD  MET B 130 "
      ideal   model   delta    sigma   weight residual
     112.70  101.59   11.11 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" N   GLN B 361 "
        pdb=" CA  GLN B 361 "
        pdb=" CB  GLN B 361 "
      ideal   model   delta    sigma   weight residual
     110.16  114.90   -4.74 1.48e+00 4.57e-01 1.02e+01
  ... (remaining 8787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.55: 3356
       15.55 -    31.11: 302
       31.11 -    46.66: 100
       46.66 -    62.21: 10
       62.21 -    77.77: 8
  Dihedral angle restraints: 3776
    sinusoidal: 1392
      harmonic: 2384
  Sorted by residual:
  dihedral pdb=" CG  ARG A 375 "
           pdb=" CD  ARG A 375 "
           pdb=" NE  ARG A 375 "
           pdb=" CZ  ARG A 375 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.34   44.66     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B 375 "
           pdb=" CD  ARG B 375 "
           pdb=" NE  ARG B 375 "
           pdb=" CZ  ARG B 375 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.40   44.60     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CA  GLN B  34 "
           pdb=" C   GLN B  34 "
           pdb=" N   ARG B  35 "
           pdb=" CA  ARG B  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.41  -14.59     0      5.00e+00 4.00e-02 8.51e+00
  ... (remaining 3773 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 798
       0.047 -    0.095: 237
       0.095 -    0.142: 49
       0.142 -    0.190: 0
       0.190 -    0.237: 2
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CB  VAL A 409 "
            pdb=" CA  VAL A 409 "
            pdb=" CG1 VAL A 409 "
            pdb=" CG2 VAL A 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  VAL B 409 "
            pdb=" CA  VAL B 409 "
            pdb=" CG1 VAL B 409 "
            pdb=" CG2 VAL B 409 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  VAL B 455 "
            pdb=" N   VAL B 455 "
            pdb=" C   VAL B 455 "
            pdb=" CB  VAL B 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.31    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 1074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 377 "    0.158 9.50e-02 1.11e+02   7.08e-02 3.24e+00
        pdb=" NE  ARG B 377 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 377 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 377 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 377 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 377 "   -0.157 9.50e-02 1.11e+02   7.05e-02 3.22e+00
        pdb=" NE  ARG A 377 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 377 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 377 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 377 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 192 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO B 193 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 193 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 193 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1071 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1028
        2.76 -     3.29: 6847
        3.29 -     3.83: 11021
        3.83 -     4.36: 12361
        4.36 -     4.90: 20329
  Nonbonded interactions: 51586
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 400 "
            pdb=" OG1 THR B 404 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   HIS A 400 "
            pdb=" OG1 THR A 404 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" NH2 ARG A 335 "
            pdb=" O   ALA A 402 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG B 335 "
            pdb=" O   ALA B 402 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   LEU B 213 "
            pdb=" OG1 THR B 216 "
     model   vdw
     2.265 3.040
  ... (remaining 51581 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.00 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:             2.080
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
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      :  0.003   0.045   6444  Z= 0.151
  Angle     :  0.717  11.116   8796  Z= 0.376
  Chirality :  0.045   0.237   1086
  Planarity :  0.005   0.071   1074
  Dihedral  : 13.859  77.767   2214
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  1.00 (0.31), residues: 802
  helix:  1.06 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -0.41 (0.52), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 377 
 TYR   0.017   0.002   TYR A 313 
 PHE   0.018   0.001   PHE A 384 
 TRP   0.006   0.001   TRP B 324 
 HIS   0.005   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6442)
  covalent geometry    : angle       0.71042 ( 8792)
  SS BOND              : bond        0.00137 (    2)
  SS BOND              : angle       4.48002 (    4)
  hydrogen bonds       : bond        0.10152 (  454)
  hydrogen bonds       : angle       4.97076 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7516 (mm110) cc_final: 0.7188 (mm110)
REVERT: A  262 GLU cc_start: 0.7075 (tp30) cc_final: 0.6673 (tp30)
REVERT: A  361 GLN cc_start: 0.6761 (mp10) cc_final: 0.6292 (mp10)
REVERT: A  377 ARG cc_start: 0.6352 (tpm170) cc_final: 0.6020 (tpm170)
REVERT: A  418 LEU cc_start: 0.8138 (tp) cc_final: 0.7903 (tp)
REVERT: A  451 MET cc_start: 0.7219 (ttp) cc_final: 0.6903 (ttp)
REVERT: B   38 SER cc_start: 0.7534 (p) cc_final: 0.7288 (p)
REVERT: B   71 GLN cc_start: 0.7508 (mm110) cc_final: 0.6852 (mm110)
REVERT: B   72 ARG cc_start: 0.7764 (tmt-80) cc_final: 0.7104 (tmt-80)
REVERT: B   85 PHE cc_start: 0.8029 (t80) cc_final: 0.7706 (t80)
REVERT: B  130 MET cc_start: 0.6429 (mtt) cc_final: 0.6165 (mtt)
REVERT: B  188 ILE cc_start: 0.8165 (tt) cc_final: 0.7847 (tt)
REVERT: B  357 LEU cc_start: 0.7020 (tt) cc_final: 0.6343 (pp)
REVERT: B  361 GLN cc_start: 0.6736 (mp10) cc_final: 0.6230 (mp10)
REVERT: B  414 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6850 (mtt-85)
REVERT: B  451 MET cc_start: 0.7030 (ttp) cc_final: 0.6699 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1145
  time to fit residues: 25.4369
Evaluate side-chains
  173 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0070
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 HIS
A 452 GLN
** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.154799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.134608 restraints weight = 10068.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.139299 restraints weight = 5099.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.142453 restraints weight = 3130.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.144773 restraints weight = 2178.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.146105 restraints weight = 1634.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6444  Z= 0.160
  Angle     :  0.655  11.207   8796  Z= 0.336
  Chirality :  0.044   0.228   1086
  Planarity :  0.005   0.041   1074
  Dihedral  :  4.178  17.266    860
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.09 %
    Favored  : 84.71 %
  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:  1.09 (0.31), residues: 802
  helix:  1.15 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -0.47 (0.52), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.019   0.002   TYR B 313 
 PHE   0.013   0.001   PHE B 459 
 TRP   0.007   0.001   TRP B 324 
 HIS   0.015   0.001   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6442)
  covalent geometry    : angle       0.65314 ( 8792)
  SS BOND              : bond        0.00293 (    2)
  SS BOND              : angle       2.51382 (    4)
  hydrogen bonds       : bond        0.04422 (  454)
  hydrogen bonds       : angle       4.37191 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7929 (mp)
REVERT: A   71 GLN cc_start: 0.7453 (mm110) cc_final: 0.7085 (mm110)
REVERT: A  262 GLU cc_start: 0.7178 (tp30) cc_final: 0.6476 (tp30)
REVERT: A  332 LEU cc_start: 0.7726 (mm) cc_final: 0.7382 (mm)
REVERT: A  357 LEU cc_start: 0.7398 (tt) cc_final: 0.7132 (tt)
REVERT: A  377 ARG cc_start: 0.6268 (tpm170) cc_final: 0.5646 (tpm170)
REVERT: A  451 MET cc_start: 0.7088 (ttp) cc_final: 0.6852 (ttp)
REVERT: B   71 GLN cc_start: 0.7492 (mm110) cc_final: 0.6800 (mm110)
REVERT: B   85 PHE cc_start: 0.8035 (t80) cc_final: 0.7715 (t80)
REVERT: B  164 PHE cc_start: 0.7028 (m-80) cc_final: 0.6780 (m-80)
REVERT: B  357 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6944 (tt)
REVERT: B  451 MET cc_start: 0.6953 (ttp) cc_final: 0.6653 (ttp)
  outliers start: 15
  outliers final: 8
  residues processed: 183
  average time/residue: 0.1037
  time to fit residues: 23.6854
Evaluate side-chains
  175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 165
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  388 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   chunk 79 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.153171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.132673 restraints weight = 9899.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.137273 restraints weight = 5013.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.140258 restraints weight = 3097.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.142493 restraints weight = 2185.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.143653 restraints weight = 1668.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6444  Z= 0.153
  Angle     :  0.636  10.065   8796  Z= 0.324
  Chirality :  0.043   0.228   1086
  Planarity :  0.004   0.041   1074
  Dihedral  :  4.062  17.843    860
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.29 %
    Favored  : 76.18 %
  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:  1.15 (0.30), residues: 802
  helix:  1.17 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -0.39 (0.53), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.019   0.002   TYR B 313 
 PHE   0.018   0.001   PHE B 459 
 TRP   0.008   0.001   TRP A 324 
 HIS   0.013   0.002   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6442)
  covalent geometry    : angle       0.63515 ( 8792)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       1.63818 (    4)
  hydrogen bonds       : bond        0.04205 (  454)
  hydrogen bonds       : angle       4.30226 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7771 (mp)
REVERT: A   71 GLN cc_start: 0.7450 (mm110) cc_final: 0.7052 (mm110)
REVERT: A   72 ARG cc_start: 0.7721 (tmt-80) cc_final: 0.7431 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7872 (mmt90)
REVERT: A  117 MET cc_start: 0.7019 (mmp) cc_final: 0.6682 (mmt)
REVERT: A  262 GLU cc_start: 0.7222 (tp30) cc_final: 0.6878 (tp30)
REVERT: A  266 ASP cc_start: 0.7910 (m-30) cc_final: 0.7619 (t0)
REVERT: A  332 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7687 (mm)
REVERT: A  357 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7299 (tp)
REVERT: A  451 MET cc_start: 0.7067 (ttp) cc_final: 0.6846 (ttp)
REVERT: A  452 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7204 (tp-100)
REVERT: B   44 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7782 (mp)
REVERT: B   71 GLN cc_start: 0.7507 (mm110) cc_final: 0.6803 (mm110)
REVERT: B   85 PHE cc_start: 0.8080 (t80) cc_final: 0.7734 (t80)
REVERT: B  332 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7787 (mm)
REVERT: B  357 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7020 (tt)
REVERT: B  383 ILE cc_start: 0.7842 (mt) cc_final: 0.7568 (tt)
REVERT: B  451 MET cc_start: 0.7009 (ttp) cc_final: 0.6690 (ttp)
REVERT: B  452 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7226 (tp-100)
  outliers start: 24
  outliers final: 12
  residues processed: 186
  average time/residue: 0.1095
  time to fit residues: 25.3706
Evaluate side-chains
  195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   chunk 63 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0370
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.2858

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 HIS
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.157728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.136025 restraints weight = 9839.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.140814 restraints weight = 4988.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.143978 restraints weight = 3092.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.145960 restraints weight = 2207.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.147414 restraints weight = 1749.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6444  Z= 0.127
  Angle     :  0.622   9.719   8796  Z= 0.310
  Chirality :  0.042   0.257   1086
  Planarity :  0.004   0.041   1074
  Dihedral  :  3.951  16.625    860
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 22.35 %
    Favored  : 73.68 %
  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:  1.14 (0.31), residues: 802
  helix:  1.09 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.23 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 183 
 TYR   0.018   0.002   TYR B 313 
 PHE   0.012   0.001   PHE B 420 
 TRP   0.011   0.001   TRP B  92 
 HIS   0.011   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6442)
  covalent geometry    : angle       0.62150 ( 8792)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       1.19457 (    4)
  hydrogen bonds       : bond        0.03922 (  454)
  hydrogen bonds       : angle       4.25934 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 170
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: A   71 GLN cc_start: 0.7438 (mm110) cc_final: 0.7041 (mm110)
REVERT: A   72 ARG cc_start: 0.7683 (tmt-80) cc_final: 0.6812 (tmt-80)
REVERT: A  117 MET cc_start: 0.7030 (mmp) cc_final: 0.6681 (mmt)
REVERT: A  262 GLU cc_start: 0.7251 (tp30) cc_final: 0.6878 (tp30)
REVERT: A  266 ASP cc_start: 0.7837 (m-30) cc_final: 0.7625 (t0)
REVERT: A  332 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7723 (mm)
REVERT: A  335 ARG cc_start: 0.6825 (ptt90) cc_final: 0.6590 (ptt90)
REVERT: A  357 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7344 (tp)
REVERT: A  451 MET cc_start: 0.7095 (ttp) cc_final: 0.6888 (ttp)
REVERT: B   44 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7651 (mp)
REVERT: B   71 GLN cc_start: 0.7512 (mm110) cc_final: 0.6812 (mm110)
REVERT: B   85 PHE cc_start: 0.8107 (t80) cc_final: 0.7726 (t80)
REVERT: B  196 CYS cc_start: 0.4681 (OUTLIER) cc_final: 0.4418 (t)
REVERT: B  332 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7770 (mm)
REVERT: B  361 GLN cc_start: 0.7009 (mp10) cc_final: 0.6804 (mp10)
REVERT: B  383 ILE cc_start: 0.7776 (mt) cc_final: 0.7508 (tt)
REVERT: B  451 MET cc_start: 0.7067 (ttp) cc_final: 0.6756 (ttp)
  outliers start: 27
  outliers final: 14
  residues processed: 179
  average time/residue: 0.1090
  time to fit residues: 24.2662
Evaluate side-chains
  182 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.151989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.130894 restraints weight = 9968.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.135534 restraints weight = 4991.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.138647 restraints weight = 3065.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.140750 restraints weight = 2153.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.142188 restraints weight = 1661.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6444  Z= 0.186
  Angle     :  0.683  10.619   8796  Z= 0.343
  Chirality :  0.044   0.284   1086
  Planarity :  0.005   0.063   1074
  Dihedral  :  4.128  20.162    860
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 22.35 %
    Favored  : 72.35 %
  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:  0.90 (0.30), residues: 802
  helix:  0.89 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.17 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  35 
 TYR   0.021   0.002   TYR B 313 
 PHE   0.017   0.001   PHE A 420 
 TRP   0.011   0.002   TRP A  92 
 HIS   0.012   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 6442)
  covalent geometry    : angle       0.67856 ( 8792)
  SS BOND              : bond        0.00826 (    2)
  SS BOND              : angle       3.76665 (    4)
  hydrogen bonds       : bond        0.04323 (  454)
  hydrogen bonds       : angle       4.41492 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: A   71 GLN cc_start: 0.7453 (mm110) cc_final: 0.7049 (mm110)
REVERT: A   72 ARG cc_start: 0.7705 (tmt-80) cc_final: 0.6743 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7367 (tp30) cc_final: 0.7119 (tp30)
REVERT: A  332 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: A  335 ARG cc_start: 0.7076 (ptt90) cc_final: 0.6788 (ptt90)
REVERT: A  362 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7931 (t)
REVERT: A  387 SER cc_start: 0.7985 (t) cc_final: 0.7681 (t)
REVERT: B   71 GLN cc_start: 0.7527 (mm110) cc_final: 0.6832 (mm110)
REVERT: B   85 PHE cc_start: 0.8105 (t80) cc_final: 0.7634 (t80)
REVERT: B  262 GLU cc_start: 0.7263 (tp30) cc_final: 0.6682 (tp30)
REVERT: B  332 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7914 (mm)
REVERT: B  357 LEU cc_start: 0.7595 (tt) cc_final: 0.7062 (tt)
REVERT: B  361 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6766 (mp10)
REVERT: B  383 ILE cc_start: 0.7862 (mt) cc_final: 0.7558 (tt)
REVERT: B  451 MET cc_start: 0.7036 (ttp) cc_final: 0.6781 (ttp)
  outliers start: 36
  outliers final: 17
  residues processed: 200
  average time/residue: 0.1013
  time to fit residues: 25.6351
Evaluate side-chains
  192 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    0.0270
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 17 optimal weight:    0.3980
   chunk 64 optimal weight:    0.0000
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.2642

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.157060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.135749 restraints weight = 9826.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.140483 restraints weight = 4968.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.143581 restraints weight = 3061.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.145727 restraints weight = 2168.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.147228 restraints weight = 1684.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6444  Z= 0.132
  Angle     :  0.652  10.104   8796  Z= 0.321
  Chirality :  0.042   0.298   1086
  Planarity :  0.004   0.042   1074
  Dihedral  :  3.946  15.713    860
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 25.29 %
    Favored  : 70.15 %
  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:  0.95 (0.31), residues: 802
  helix:  0.98 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.42 (0.56), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  35 
 TYR   0.019   0.002   TYR B 313 
 PHE   0.016   0.001   PHE A 420 
 TRP   0.017   0.002   TRP B  92 
 HIS   0.011   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6442)
  covalent geometry    : angle       0.64780 ( 8792)
  SS BOND              : bond        0.00629 (    2)
  SS BOND              : angle       3.64834 (    4)
  hydrogen bonds       : bond        0.03906 (  454)
  hydrogen bonds       : angle       4.31192 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7439 (mm110) cc_final: 0.7030 (mm110)
REVERT: A   72 ARG cc_start: 0.7659 (tmt-80) cc_final: 0.6654 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7306 (tp30) cc_final: 0.7065 (tp30)
REVERT: A  266 ASP cc_start: 0.7859 (m-30) cc_final: 0.7608 (t0)
REVERT: A  332 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7777 (mm)
REVERT: A  335 ARG cc_start: 0.6944 (ptt90) cc_final: 0.6641 (ptt90)
REVERT: A  361 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6432 (mt0)
REVERT: A  362 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7903 (t)
REVERT: A  387 SER cc_start: 0.7976 (t) cc_final: 0.7617 (t)
REVERT: B   71 GLN cc_start: 0.7505 (mm110) cc_final: 0.6804 (mm110)
REVERT: B   85 PHE cc_start: 0.8146 (t80) cc_final: 0.7674 (t80)
REVERT: B  332 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7919 (mm)
REVERT: B  349 LEU cc_start: 0.7432 (mt) cc_final: 0.7173 (mp)
REVERT: B  357 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6871 (tt)
REVERT: B  361 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6599 (mp10)
REVERT: B  383 ILE cc_start: 0.7783 (mt) cc_final: 0.7473 (tt)
REVERT: B  451 MET cc_start: 0.7034 (ttp) cc_final: 0.6717 (ttp)
  outliers start: 31
  outliers final: 17
  residues processed: 184
  average time/residue: 0.1026
  time to fit residues: 23.6552
Evaluate side-chains
  195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0770
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.155302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.133788 restraints weight = 9818.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.138485 restraints weight = 4983.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.141648 restraints weight = 3076.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.143723 restraints weight = 2173.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.145172 restraints weight = 1693.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6444  Z= 0.150
  Angle     :  0.663  10.552   8796  Z= 0.325
  Chirality :  0.042   0.262   1086
  Planarity :  0.004   0.039   1074
  Dihedral  :  3.934  16.489    860
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.47 %
    Favored  : 68.97 %
  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:  0.93 (0.31), residues: 802
  helix:  0.99 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.50 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  35 
 TYR   0.020   0.002   TYR B 313 
 PHE   0.016   0.001   PHE B 420 
 TRP   0.015   0.001   TRP B  92 
 HIS   0.014   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6442)
  covalent geometry    : angle       0.65986 ( 8792)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       2.95410 (    4)
  hydrogen bonds       : bond        0.03988 (  454)
  hydrogen bonds       : angle       4.30976 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7459 (mm110) cc_final: 0.7049 (mm110)
REVERT: A   72 ARG cc_start: 0.7698 (tmt-80) cc_final: 0.6685 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7823 (mmt90)
REVERT: A  262 GLU cc_start: 0.7305 (tp30) cc_final: 0.7073 (tp30)
REVERT: A  266 ASP cc_start: 0.7862 (m-30) cc_final: 0.7620 (t0)
REVERT: A  332 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7807 (mm)
REVERT: A  335 ARG cc_start: 0.6987 (ptt90) cc_final: 0.6680 (ptt90)
REVERT: A  362 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7903 (t)
REVERT: A  387 SER cc_start: 0.7957 (t) cc_final: 0.7666 (t)
REVERT: B   71 GLN cc_start: 0.7520 (mm110) cc_final: 0.6813 (mm110)
REVERT: B   85 PHE cc_start: 0.8202 (t80) cc_final: 0.7698 (t80)
REVERT: B  332 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (mm)
REVERT: B  357 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6821 (tt)
REVERT: B  361 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6614 (mp10)
REVERT: B  383 ILE cc_start: 0.7827 (mt) cc_final: 0.7519 (tt)
REVERT: B  451 MET cc_start: 0.7037 (ttp) cc_final: 0.6782 (ttp)
  outliers start: 31
  outliers final: 18
  residues processed: 189
  average time/residue: 0.0949
  time to fit residues: 22.4385
Evaluate side-chains
  201 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 7 optimal weight:    0.4980
   chunk 71 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.154646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.133116 restraints weight = 9791.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.137744 restraints weight = 4983.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.140786 restraints weight = 3094.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.142812 restraints weight = 2209.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.144294 restraints weight = 1734.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6444  Z= 0.173
  Angle     :  0.696  11.172   8796  Z= 0.343
  Chirality :  0.043   0.233   1086
  Planarity :  0.004   0.039   1074
  Dihedral  :  4.023  17.435    860
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 27.94 %
    Favored  : 67.79 %
  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:  0.88 (0.30), residues: 802
  helix:  0.84 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.08 (0.60), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  35 
 TYR   0.021   0.002   TYR B 313 
 PHE   0.016   0.001   PHE B 420 
 TRP   0.021   0.002   TRP B  92 
 HIS   0.016   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6442)
  covalent geometry    : angle       0.69390 ( 8792)
  SS BOND              : bond        0.00727 (    2)
  SS BOND              : angle       2.62994 (    4)
  hydrogen bonds       : bond        0.04148 (  454)
  hydrogen bonds       : angle       4.37673 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7480 (mm110) cc_final: 0.7068 (mm110)
REVERT: A   72 ARG cc_start: 0.7680 (tmt-80) cc_final: 0.6704 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7723 (mmt90)
REVERT: A  262 GLU cc_start: 0.7299 (tp30) cc_final: 0.7046 (tp30)
REVERT: A  266 ASP cc_start: 0.7836 (m-30) cc_final: 0.7625 (t0)
REVERT: A  332 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7833 (mm)
REVERT: A  335 ARG cc_start: 0.6995 (ptt90) cc_final: 0.6718 (ptt90)
REVERT: A  362 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8022 (t)
REVERT: A  387 SER cc_start: 0.7991 (t) cc_final: 0.7648 (t)
REVERT: B   71 GLN cc_start: 0.7512 (mm110) cc_final: 0.6799 (mm110)
REVERT: B   77 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7691 (mtt90)
REVERT: B   85 PHE cc_start: 0.8166 (t80) cc_final: 0.7676 (t80)
REVERT: B  262 GLU cc_start: 0.7201 (tp30) cc_final: 0.6807 (tp30)
REVERT: B  332 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (mm)
REVERT: B  357 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6941 (tt)
REVERT: B  361 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6637 (mp10)
REVERT: B  383 ILE cc_start: 0.7854 (mt) cc_final: 0.7538 (tt)
REVERT: B  451 MET cc_start: 0.6992 (ttp) cc_final: 0.6776 (ttp)
  outliers start: 29
  outliers final: 19
  residues processed: 194
  average time/residue: 0.0963
  time to fit residues: 23.6919
Evaluate side-chains
  207 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0020
   chunk 2 optimal weight:    0.0970
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.155696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.134301 restraints weight = 9951.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.139019 restraints weight = 4932.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.142156 restraints weight = 3012.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.144222 restraints weight = 2128.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.145690 restraints weight = 1653.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   6444  Z= 0.162
  Angle     :  0.709  11.663   8796  Z= 0.347
  Chirality :  0.045   0.346   1086
  Planarity :  0.004   0.039   1074
  Dihedral  :  4.028  16.747    860
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.79 %
    Favored  : 67.35 %
  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:  0.81 (0.31), residues: 802
  helix:  0.80 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.13 (0.60), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 309 
 TYR   0.022   0.002   TYR B 313 
 PHE   0.018   0.001   PHE B 420 
 TRP   0.023   0.002   TRP B  92 
 HIS   0.018   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6442)
  covalent geometry    : angle       0.70637 ( 8792)
  SS BOND              : bond        0.00442 (    2)
  SS BOND              : angle       3.09477 (    4)
  hydrogen bonds       : bond        0.04091 (  454)
  hydrogen bonds       : angle       4.37457 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7592 (mm)
REVERT: A   71 GLN cc_start: 0.7490 (mm110) cc_final: 0.7075 (mm110)
REVERT: A   72 ARG cc_start: 0.7690 (tmt-80) cc_final: 0.6704 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7261 (tp30) cc_final: 0.7015 (tp30)
REVERT: A  332 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (mm)
REVERT: A  335 ARG cc_start: 0.6974 (ptt90) cc_final: 0.6695 (ptt90)
REVERT: A  347 LEU cc_start: 0.8323 (mp) cc_final: 0.7884 (mm)
REVERT: A  362 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7999 (t)
REVERT: A  387 SER cc_start: 0.7946 (t) cc_final: 0.7597 (t)
REVERT: B   71 GLN cc_start: 0.7522 (mm110) cc_final: 0.6818 (mm110)
REVERT: B   85 PHE cc_start: 0.8160 (t80) cc_final: 0.7620 (t80)
REVERT: B  262 GLU cc_start: 0.7298 (tp30) cc_final: 0.6877 (tp30)
REVERT: B  332 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7918 (mm)
REVERT: B  383 ILE cc_start: 0.7827 (mt) cc_final: 0.7506 (tt)
REVERT: B  451 MET cc_start: 0.7060 (ttp) cc_final: 0.6831 (ttp)
  outliers start: 33
  outliers final: 24
  residues processed: 194
  average time/residue: 0.0988
  time to fit residues: 24.2385
Evaluate side-chains
  210 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  357 LEU
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0070
   chunk 28 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** 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 = 0.4140 r_free = 0.4140 target = 0.156898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.135248 restraints weight = 9790.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139980 restraints weight = 4904.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.143132 restraints weight = 3005.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.145231 restraints weight = 2124.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.146662 restraints weight = 1654.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6444  Z= 0.165
  Angle     :  0.717  12.115   8796  Z= 0.353
  Chirality :  0.044   0.351   1086
  Planarity :  0.005   0.038   1074
  Dihedral  :  4.126  17.183    860
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.53 %
    Favored  : 66.91 %
  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:  0.82 (0.31), residues: 802
  helix:  0.79 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.10 (0.60), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  35 
 TYR   0.022   0.002   TYR B 313 
 PHE   0.022   0.001   PHE B 420 
 TRP   0.023   0.002   TRP B  92 
 HIS   0.016   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6442)
  covalent geometry    : angle       0.71492 ( 8792)
  SS BOND              : bond        0.00636 (    2)
  SS BOND              : angle       2.65599 (    4)
  hydrogen bonds       : bond        0.04111 (  454)
  hydrogen bonds       : angle       4.38582 ( 1350)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 187
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7583 (mm)
REVERT: A   71 GLN cc_start: 0.7475 (mm110) cc_final: 0.7064 (mm110)
REVERT: A   72 ARG cc_start: 0.7654 (tmt-80) cc_final: 0.6651 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7255 (tp30) cc_final: 0.7032 (tp30)
REVERT: A  332 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7815 (mm)
REVERT: A  335 ARG cc_start: 0.6981 (ptt90) cc_final: 0.6680 (ptt90)
REVERT: A  362 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7963 (t)
REVERT: A  387 SER cc_start: 0.7899 (t) cc_final: 0.7581 (t)
REVERT: B   71 GLN cc_start: 0.7528 (mm110) cc_final: 0.6800 (mm110)
REVERT: B   77 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7626 (mtt90)
REVERT: B   85 PHE cc_start: 0.8160 (t80) cc_final: 0.7636 (t80)
REVERT: B  262 GLU cc_start: 0.7188 (tp30) cc_final: 0.6433 (tp30)
REVERT: B  332 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7941 (mm)
REVERT: B  383 ILE cc_start: 0.7835 (mt) cc_final: 0.7524 (tt)
REVERT: B  451 MET cc_start: 0.7067 (ttp) cc_final: 0.6845 (ttp)
  outliers start: 31
  outliers final: 23
  residues processed: 197
  average time/residue: 0.1053
  time to fit residues: 26.1817
Evaluate side-chains
  211 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  420 PHE
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  191 GLN
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  314 PHE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  420 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    0.0060
   chunk 54 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0010
   chunk 21 optimal weight:    0.0980
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   overall best weight:    0.1802

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 416 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.158719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.137241 restraints weight = 9881.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.141965 restraints weight = 4901.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.145118 restraints weight = 2997.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.147208 restraints weight = 2114.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.148665 restraints weight = 1644.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6444  Z= 0.141
  Angle     :  0.694  11.908   8796  Z= 0.338
  Chirality :  0.043   0.347   1086
  Planarity :  0.005   0.045   1074
  Dihedral  :  4.078  16.313    860
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 27.79 %
    Favored  : 67.06 %
  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:  0.92 (0.31), residues: 802
  helix:  0.89 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.18 (0.59), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 309 
 TYR   0.021   0.002   TYR B 313 
 PHE   0.020   0.001   PHE B 420 
 TRP   0.021   0.002   TRP B  92 
 HIS   0.015   0.002   HIS B 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6442)
  covalent geometry    : angle       0.69240 ( 8792)
  SS BOND              : bond        0.00371 (    2)
  SS BOND              : angle       2.17501 (    4)
  hydrogen bonds       : bond        0.03965 (  454)
  hydrogen bonds       : angle       4.33772 ( 1350)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1251.55 seconds
wall clock time: 22 minutes 18.51 seconds (1338.51 seconds total)