Starting phenix.real_space_refine
on Tue Mar 11 16:04:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_23300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_23300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_23300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_23300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lf6_23300/03_2025/7lf6_23300.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.45, per 1000 atoms: 0.87
  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: 1.48
  Conformation dependent library (CDL) restraints added in 860.3 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: 0.50
  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: 1.60

  Time building geometry restraints manager: 1.78 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: 0.03
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:             1.720
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.610
-------------------------------------------------------------------------------
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   6442  Z= 0.211
  Angle     :  0.710  11.116   8792  Z= 0.374
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.006   0.001   TRP B 324 
 HIS   0.005   0.001   HIS A 416 
 PHE   0.018   0.001   PHE A 384 
 TYR   0.017   0.002   TYR A 313 
 ARG   0.007   0.001   ARG A 377 

*********************** 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  : 0.660 
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: 0.7904 (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: 0.6698 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2411
  time to fit residues: 53.4991
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  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0070
   chunk 46 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.153879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.133772 restraints weight = 9879.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.138453 restraints weight = 4976.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.141410 restraints weight = 3051.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6442  Z= 0.235
  Angle     :  0.668  11.692   8792  Z= 0.342
  Chirality :  0.045   0.230   1086
  Planarity :  0.005   0.040   1074
  Dihedral  :  4.240  18.775    860
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.97 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.30), residues: 802
  helix:  1.09 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -0.43 (0.52), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 410 
 HIS   0.013   0.001   HIS B 449 
 PHE   0.014   0.001   PHE B 459 
 TYR   0.019   0.002   TYR B 313 
 ARG   0.006   0.001   ARG B  35 

*********************** 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
  204 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (mp)
REVERT: A   71 GLN cc_start: 0.7530 (mm110) cc_final: 0.7151 (mm110)
REVERT: A   77 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7875 (mmt90)
REVERT: A  262 GLU cc_start: 0.7232 (tp30) cc_final: 0.6543 (tp30)
REVERT: A  332 LEU cc_start: 0.7757 (mm) cc_final: 0.7432 (mm)
REVERT: A  335 ARG cc_start: 0.6804 (ptt90) cc_final: 0.6589 (ptt90)
REVERT: A  357 LEU cc_start: 0.7428 (tt) cc_final: 0.7161 (tt)
REVERT: A  377 ARG cc_start: 0.6271 (tpm170) cc_final: 0.5638 (tpm170)
REVERT: A  416 HIS cc_start: 0.7383 (t-90) cc_final: 0.7085 (t-170)
REVERT: A  451 MET cc_start: 0.7215 (ttp) cc_final: 0.6966 (ttp)
REVERT: A  452 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7465 (tp-100)
REVERT: B   71 GLN cc_start: 0.7552 (mm110) cc_final: 0.6856 (mm110)
REVERT: B   85 PHE cc_start: 0.8064 (t80) cc_final: 0.7759 (t80)
REVERT: B  164 PHE cc_start: 0.7072 (m-80) cc_final: 0.6826 (m-80)
REVERT: B  357 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6943 (tt)
REVERT: B  451 MET cc_start: 0.7099 (ttp) cc_final: 0.6752 (ttp)
  outliers start: 16
  outliers final: 9
  residues processed: 191
  average time/residue: 0.2235
  time to fit residues: 53.6258
Evaluate side-chains
  185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  276 LEU
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 4 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   overall best weight:    0.4078

-------------------------------------------------------------------------------
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 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.153989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.133406 restraints weight = 9906.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.138186 restraints weight = 4903.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.141398 restraints weight = 2966.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6442  Z= 0.192
  Angle     :  0.628   9.805   8792  Z= 0.318
  Chirality :  0.043   0.225   1086
  Planarity :  0.004   0.042   1074
  Dihedral  :  4.030  17.277    860
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.32 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.31), residues: 802
  helix:  1.19 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -0.37 (0.53), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  92 
 HIS   0.016   0.001   HIS A 449 
 PHE   0.018   0.001   PHE B 459 
 TYR   0.019   0.002   TYR B 313 
 ARG   0.008   0.001   ARG B  35 

*********************** 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
  206 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7856 (mp)
REVERT: A   71 GLN cc_start: 0.7515 (mm110) cc_final: 0.7123 (mm110)
REVERT: A   72 ARG cc_start: 0.7792 (tmt-80) cc_final: 0.7566 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7881 (mmt90)
REVERT: A  117 MET cc_start: 0.7076 (mmp) cc_final: 0.6744 (mmt)
REVERT: A  262 GLU cc_start: 0.7263 (tp30) cc_final: 0.6899 (tp30)
REVERT: A  266 ASP cc_start: 0.7929 (m-30) cc_final: 0.7726 (t0)
REVERT: A  332 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7686 (mm)
REVERT: A  357 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7240 (tp)
REVERT: A  416 HIS cc_start: 0.7402 (t-90) cc_final: 0.7144 (t-170)
REVERT: A  451 MET cc_start: 0.7202 (ttp) cc_final: 0.6958 (ttp)
REVERT: A  452 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7226 (tp-100)
REVERT: B   44 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (mp)
REVERT: B   71 GLN cc_start: 0.7547 (mm110) cc_final: 0.6836 (mm110)
REVERT: B   85 PHE cc_start: 0.8086 (t80) cc_final: 0.7723 (t80)
REVERT: B  332 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7769 (mm)
REVERT: B  357 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6942 (tt)
REVERT: B  383 ILE cc_start: 0.7785 (mt) cc_final: 0.7511 (tt)
REVERT: B  451 MET cc_start: 0.7117 (ttp) cc_final: 0.6787 (ttp)
  outliers start: 25
  outliers final: 10
  residues processed: 187
  average time/residue: 0.2223
  time to fit residues: 51.8031
Evaluate side-chains
  195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  462 LEU
Chi-restraints excluded: chain B residue   44 LEU
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  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 72 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0070
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0000
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4602

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.155148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.133771 restraints weight = 9901.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.138406 restraints weight = 4968.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.141581 restraints weight = 3084.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6442  Z= 0.206
  Angle     :  0.642   9.754   8792  Z= 0.322
  Chirality :  0.043   0.255   1086
  Planarity :  0.004   0.040   1074
  Dihedral  :  4.005  17.156    860
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.35 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 802
  helix:  1.04 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.24 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  92 
 HIS   0.012   0.002   HIS B 449 
 PHE   0.014   0.001   PHE B 420 
 TYR   0.019   0.002   TYR B 313 
 ARG   0.004   0.000   ARG B  35 

*********************** 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
  201 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7806 (mp)
REVERT: A   55 VAL cc_start: 0.8737 (t) cc_final: 0.8481 (p)
REVERT: A   71 GLN cc_start: 0.7522 (mm110) cc_final: 0.7121 (mm110)
REVERT: A   72 ARG cc_start: 0.7777 (tmt-80) cc_final: 0.7520 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7932 (mmt90)
REVERT: A  117 MET cc_start: 0.7098 (mmp) cc_final: 0.6721 (mmt)
REVERT: A  262 GLU cc_start: 0.7231 (tp30) cc_final: 0.6990 (tp30)
REVERT: A  332 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7785 (mm)
REVERT: A  335 ARG cc_start: 0.6935 (ptt90) cc_final: 0.6726 (ptt90)
REVERT: A  357 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7191 (tt)
REVERT: A  416 HIS cc_start: 0.7565 (t-90) cc_final: 0.7248 (t-170)
REVERT: A  451 MET cc_start: 0.7193 (ttp) cc_final: 0.6982 (ttp)
REVERT: B   44 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: B   71 GLN cc_start: 0.7567 (mm110) cc_final: 0.6862 (mm110)
REVERT: B   85 PHE cc_start: 0.8116 (t80) cc_final: 0.7714 (t80)
REVERT: B  196 CYS cc_start: 0.4832 (OUTLIER) cc_final: 0.4553 (t)
REVERT: B  332 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7784 (mm)
REVERT: B  357 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6890 (tt)
REVERT: B  361 GLN cc_start: 0.7028 (mp10) cc_final: 0.6743 (mp10)
REVERT: B  383 ILE cc_start: 0.7807 (mt) cc_final: 0.7529 (tt)
REVERT: B  451 MET cc_start: 0.7176 (ttp) cc_final: 0.6866 (ttp)
  outliers start: 25
  outliers final: 13
  residues processed: 183
  average time/residue: 0.2354
  time to fit residues: 53.7643
Evaluate side-chains
  192 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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  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  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  414 ARG
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  196 CYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 79 optimal weight:    0.0770
   chunk 61 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0970
   overall best weight:    0.1936

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.158295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.136895 restraints weight = 9922.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.141655 restraints weight = 5020.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.144822 restraints weight = 3093.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6442  Z= 0.168
  Angle     :  0.614   9.487   8792  Z= 0.304
  Chirality :  0.041   0.273   1086
  Planarity :  0.004   0.041   1074
  Dihedral  :  3.876  16.736    860
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 23.38 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.31), residues: 802
  helix:  1.14 (0.21), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.50 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  92 
 HIS   0.012   0.001   HIS B 449 
 PHE   0.013   0.001   PHE A 420 
 TYR   0.018   0.002   TYR B 313 
 ARG   0.002   0.000   ARG B 377 

*********************** 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
  204 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7876 (p)
REVERT: A   44 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7729 (mp)
REVERT: A   55 VAL cc_start: 0.8715 (t) cc_final: 0.8481 (p)
REVERT: A   71 GLN cc_start: 0.7523 (mm110) cc_final: 0.7105 (mm110)
REVERT: A   72 ARG cc_start: 0.7757 (tmt-80) cc_final: 0.7481 (tmt-80)
REVERT: A  117 MET cc_start: 0.7031 (mmp) cc_final: 0.6637 (mmt)
REVERT: A  182 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8448 (mmt-90)
REVERT: A  262 GLU cc_start: 0.7151 (tp30) cc_final: 0.6940 (tp30)
REVERT: A  332 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7752 (mm)
REVERT: A  357 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7353 (tp)
REVERT: A  387 SER cc_start: 0.7985 (t) cc_final: 0.7689 (t)
REVERT: A  416 HIS cc_start: 0.7547 (t-90) cc_final: 0.7218 (t-170)
REVERT: B   44 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7677 (mp)
REVERT: B   71 GLN cc_start: 0.7543 (mm110) cc_final: 0.6834 (mm110)
REVERT: B   85 PHE cc_start: 0.8140 (t80) cc_final: 0.7735 (t80)
REVERT: B  196 CYS cc_start: 0.4785 (OUTLIER) cc_final: 0.4508 (t)
REVERT: B  332 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7732 (mm)
REVERT: B  357 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6777 (tt)
REVERT: B  361 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6605 (mp10)
REVERT: B  383 ILE cc_start: 0.7728 (mt) cc_final: 0.7465 (tt)
REVERT: B  451 MET cc_start: 0.7131 (ttp) cc_final: 0.6789 (ttp)
  outliers start: 33
  outliers final: 11
  residues processed: 185
  average time/residue: 0.2553
  time to fit residues: 59.0717
Evaluate side-chains
  186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   40 SER
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  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  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  196 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    0.2980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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  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 = 0.4110 r_free = 0.4110 target = 0.155178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.133355 restraints weight = 9794.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.137978 restraints weight = 5020.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.141123 restraints weight = 3148.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6442  Z= 0.230
  Angle     :  0.658   9.909   8792  Z= 0.326
  Chirality :  0.043   0.306   1086
  Planarity :  0.004   0.039   1074
  Dihedral  :  3.917  17.233    860
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 24.12 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 802
  helix:  1.05 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.29 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  92 
 HIS   0.014   0.002   HIS B 449 
 PHE   0.016   0.001   PHE B 420 
 TYR   0.020   0.002   TYR B 313 
 ARG   0.005   0.000   ARG A  35 

*********************** 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
  215 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 179
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: A   71 GLN cc_start: 0.7529 (mm110) cc_final: 0.7129 (mm110)
REVERT: A   72 ARG cc_start: 0.7767 (tmt-80) cc_final: 0.6751 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7351 (tp30) cc_final: 0.7088 (tp30)
REVERT: A  329 SER cc_start: 0.8501 (p) cc_final: 0.8268 (p)
REVERT: A  332 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7781 (mm)
REVERT: A  357 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7012 (tt)
REVERT: A  361 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6691 (mp10)
REVERT: A  387 SER cc_start: 0.7988 (t) cc_final: 0.7665 (t)
REVERT: A  416 HIS cc_start: 0.7706 (t-90) cc_final: 0.7488 (t-170)
REVERT: B   44 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7741 (mp)
REVERT: B   71 GLN cc_start: 0.7570 (mm110) cc_final: 0.6861 (mm110)
REVERT: B   85 PHE cc_start: 0.8184 (t80) cc_final: 0.7729 (t80)
REVERT: B  196 CYS cc_start: 0.4870 (OUTLIER) cc_final: 0.4590 (t)
REVERT: B  332 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7798 (mm)
REVERT: B  357 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6841 (tt)
REVERT: B  361 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6649 (mp10)
REVERT: B  383 ILE cc_start: 0.7809 (mt) cc_final: 0.7513 (tt)
REVERT: B  451 MET cc_start: 0.7181 (ttp) cc_final: 0.6877 (ttp)
  outliers start: 36
  outliers final: 15
  residues processed: 191
  average time/residue: 0.2475
  time to fit residues: 59.5499
Evaluate side-chains
  199 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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  163 HIS
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  361 GLN
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  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain B residue   44 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  196 CYS
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  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 24 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   chunk 78 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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  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 = 0.4103 r_free = 0.4103 target = 0.154728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.133348 restraints weight = 9862.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.137923 restraints weight = 5033.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.140998 restraints weight = 3129.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6442  Z= 0.230
  Angle     :  0.681  10.277   8792  Z= 0.331
  Chirality :  0.043   0.260   1086
  Planarity :  0.004   0.039   1074
  Dihedral  :  3.941  17.012    860
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 25.44 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.30), residues: 802
  helix:  0.97 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.52 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  92 
 HIS   0.014   0.002   HIS B 449 
 PHE   0.016   0.001   PHE B 420 
 TYR   0.020   0.002   TYR B 313 
 ARG   0.004   0.000   ARG A  35 

*********************** 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
  214 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 179
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: A   71 GLN cc_start: 0.7551 (mm110) cc_final: 0.7146 (mm110)
REVERT: A   72 ARG cc_start: 0.7763 (tmt-80) cc_final: 0.6750 (tmt-80)
REVERT: A  262 GLU cc_start: 0.7352 (tp30) cc_final: 0.7094 (tp30)
REVERT: A  332 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7790 (mm)
REVERT: A  361 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6839 (mp10)
REVERT: A  387 SER cc_start: 0.7964 (t) cc_final: 0.7622 (t)
REVERT: A  416 HIS cc_start: 0.7737 (t-90) cc_final: 0.7449 (t-170)
REVERT: B   44 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7844 (mp)
REVERT: B   71 GLN cc_start: 0.7572 (mm110) cc_final: 0.6863 (mm110)
REVERT: B   85 PHE cc_start: 0.8157 (t80) cc_final: 0.7669 (t80)
REVERT: B  196 CYS cc_start: 0.4846 (OUTLIER) cc_final: 0.4567 (t)
REVERT: B  332 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7805 (mm)
REVERT: B  357 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6798 (tt)
REVERT: B  361 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6610 (mp10)
REVERT: B  383 ILE cc_start: 0.7812 (mt) cc_final: 0.7513 (tt)
REVERT: B  451 MET cc_start: 0.7187 (ttp) cc_final: 0.6911 (ttp)
  outliers start: 35
  outliers final: 20
  residues processed: 190
  average time/residue: 0.2297
  time to fit residues: 54.8586
Evaluate side-chains
  206 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  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  314 PHE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  335 ARG
Chi-restraints excluded: chain A residue  361 GLN
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  452 GLN
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   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  196 CYS
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 35 optimal weight:    0.9990
   chunk 76 optimal weight:    0.1980
   chunk 3 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6342

-------------------------------------------------------------------------------
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  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 = 0.4089 r_free = 0.4089 target = 0.153456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.132192 restraints weight = 9799.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.136780 restraints weight = 5011.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.139798 restraints weight = 3136.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6442  Z= 0.258
  Angle     :  0.709  11.469   8792  Z= 0.349
  Chirality :  0.045   0.337   1086
  Planarity :  0.005   0.052   1074
  Dihedral  :  4.071  18.279    860
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 25.88 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.31), residues: 802
  helix:  0.87 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.53 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  92 
 HIS   0.015   0.002   HIS B 449 
 PHE   0.016   0.001   PHE B 420 
 TYR   0.022   0.002   TYR B 313 
 ARG   0.008   0.000   ARG A  35 

*********************** 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
  220 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 181
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.6915 (tp-100) cc_final: 0.6607 (tp-100)
REVERT: A   40 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7946 (p)
REVERT: A   44 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: A   71 GLN cc_start: 0.7556 (mm110) cc_final: 0.7139 (mm110)
REVERT: A   72 ARG cc_start: 0.7771 (tmt-80) cc_final: 0.6752 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7766 (mtt90)
REVERT: A  262 GLU cc_start: 0.7402 (tp30) cc_final: 0.7122 (tp30)
REVERT: A  329 SER cc_start: 0.8396 (p) cc_final: 0.8186 (p)
REVERT: A  332 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: A  387 SER cc_start: 0.7943 (t) cc_final: 0.7643 (t)
REVERT: A  416 HIS cc_start: 0.7809 (t-90) cc_final: 0.7473 (t-170)
REVERT: B   71 GLN cc_start: 0.7580 (mm110) cc_final: 0.6873 (mm110)
REVERT: B   85 PHE cc_start: 0.8165 (t80) cc_final: 0.7651 (t80)
REVERT: B  196 CYS cc_start: 0.4855 (OUTLIER) cc_final: 0.4582 (t)
REVERT: B  262 GLU cc_start: 0.7202 (tp30) cc_final: 0.6732 (tp30)
REVERT: B  332 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7796 (mm)
REVERT: B  357 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7176 (tt)
REVERT: B  361 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6826 (mp10)
REVERT: B  383 ILE cc_start: 0.7830 (mt) cc_final: 0.7513 (tt)
REVERT: B  451 MET cc_start: 0.7200 (ttp) cc_final: 0.6932 (ttp)
  outliers start: 39
  outliers final: 24
  residues processed: 197
  average time/residue: 0.2244
  time to fit residues: 55.1318
Evaluate side-chains
  210 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   40 SER
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  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  335 ARG
Chi-restraints excluded: chain A residue  351 PHE
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  423 LEU
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  196 CYS
Chi-restraints excluded: chain B residue  276 LEU
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  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 33 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0270
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.155964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.134315 restraints weight = 9911.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.139034 restraints weight = 4953.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.142227 restraints weight = 3045.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6442  Z= 0.245
  Angle     :  0.701  11.711   8792  Z= 0.346
  Chirality :  0.046   0.386   1086
  Planarity :  0.004   0.040   1074
  Dihedral  :  4.096  17.898    860
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.31), residues: 802
  helix:  0.87 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -0.55 (0.57), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  92 
 HIS   0.017   0.002   HIS B 449 
 PHE   0.016   0.001   PHE B 420 
 TYR   0.022   0.002   TYR B 313 
 ARG   0.006   0.000   ARG A  35 

*********************** 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
  219 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.6938 (tp-100) cc_final: 0.6631 (tp-100)
REVERT: A   44 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (mp)
REVERT: A   71 GLN cc_start: 0.7566 (mm110) cc_final: 0.7138 (mm110)
REVERT: A   72 ARG cc_start: 0.7751 (tmt-80) cc_final: 0.6738 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7751 (mtt90)
REVERT: A  262 GLU cc_start: 0.7397 (tp30) cc_final: 0.7136 (tp30)
REVERT: A  332 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (mm)
REVERT: A  387 SER cc_start: 0.7943 (t) cc_final: 0.7624 (t)
REVERT: A  416 HIS cc_start: 0.7798 (t-90) cc_final: 0.7449 (t-170)
REVERT: B   71 GLN cc_start: 0.7576 (mm110) cc_final: 0.6853 (mm110)
REVERT: B   77 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7723 (mtt90)
REVERT: B   85 PHE cc_start: 0.8200 (t80) cc_final: 0.7660 (t80)
REVERT: B  196 CYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4553 (t)
REVERT: B  262 GLU cc_start: 0.7214 (tp30) cc_final: 0.6747 (tp30)
REVERT: B  332 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7776 (mm)
REVERT: B  357 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6918 (tt)
REVERT: B  361 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6637 (mp10)
REVERT: B  383 ILE cc_start: 0.7817 (mt) cc_final: 0.7502 (tt)
REVERT: B  451 MET cc_start: 0.7196 (ttp) cc_final: 0.6930 (ttp)
  outliers start: 33
  outliers final: 22
  residues processed: 198
  average time/residue: 0.2229
  time to fit residues: 55.4207
Evaluate side-chains
  212 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  335 ARG
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
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   47 ILE
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  276 LEU
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  355 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0770
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0470
   chunk 37 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.4036

-------------------------------------------------------------------------------
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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.157164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.135604 restraints weight = 9786.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.140383 restraints weight = 4919.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.143584 restraints weight = 3013.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6442  Z= 0.217
  Angle     :  0.684  12.090   8792  Z= 0.337
  Chirality :  0.045   0.393   1086
  Planarity :  0.004   0.041   1074
  Dihedral  :  4.059  16.988    860
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 27.50 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.31), residues: 802
  helix:  0.89 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.14 (0.60), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  92 
 HIS   0.016   0.002   HIS B 449 
 PHE   0.020   0.001   PHE B 420 
 TYR   0.021   0.002   TYR B 313 
 ARG   0.008   0.000   ARG B 309 

********************** 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
  206 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7887 (mp)
REVERT: A   71 GLN cc_start: 0.7555 (mm110) cc_final: 0.7138 (mm110)
REVERT: A   72 ARG cc_start: 0.7736 (tmt-80) cc_final: 0.6705 (tmt-80)
REVERT: A   77 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7815 (mtt90)
REVERT: A  182 ARG cc_start: 0.8749 (mmp80) cc_final: 0.8406 (mmt-90)
REVERT: A  196 CYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4241 (t)
REVERT: A  262 GLU cc_start: 0.7373 (tp30) cc_final: 0.7131 (tp30)
REVERT: A  332 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7777 (mm)
REVERT: A  361 GLN cc_start: 0.7423 (mp10) cc_final: 0.7144 (mp10)
REVERT: A  387 SER cc_start: 0.7915 (t) cc_final: 0.7612 (t)
REVERT: A  416 HIS cc_start: 0.7804 (t-90) cc_final: 0.7454 (t-90)
REVERT: B   71 GLN cc_start: 0.7568 (mm110) cc_final: 0.6841 (mm110)
REVERT: B   77 ARG cc_start: 0.8000 (mmt90) cc_final: 0.7722 (mtt90)
REVERT: B   85 PHE cc_start: 0.8227 (t80) cc_final: 0.7698 (t80)
REVERT: B  196 CYS cc_start: 0.4783 (OUTLIER) cc_final: 0.4431 (t)
REVERT: B  332 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (mm)
REVERT: B  357 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6955 (tp)
REVERT: B  361 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6537 (mp10)
REVERT: B  383 ILE cc_start: 0.7789 (mt) cc_final: 0.7477 (tt)
REVERT: B  451 MET cc_start: 0.7183 (ttp) cc_final: 0.6926 (ttp)
  outliers start: 30
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2321
  time to fit residues: 53.8959
Evaluate side-chains
  200 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
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  163 HIS
Chi-restraints excluded: chain A residue  178 ARG
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  196 CYS
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  314 PHE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  335 ARG
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  462 LEU
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  196 CYS
Chi-restraints excluded: chain B residue  276 LEU
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  355 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.155123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.133471 restraints weight = 9960.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.138240 restraints weight = 4968.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.141368 restraints weight = 3035.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6442  Z= 0.283
  Angle     :  0.709  12.869   8792  Z= 0.353
  Chirality :  0.046   0.386   1086
  Planarity :  0.005   0.041   1074
  Dihedral  :  4.124  19.176    860
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 27.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.31), residues: 802
  helix:  0.82 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.13 (0.60), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  92 
 HIS   0.014   0.002   HIS B 449 
 PHE   0.020   0.001   PHE B 420 
 TYR   0.023   0.002   TYR B 313 
 ARG   0.006   0.001   ARG B 309 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2346.40 seconds
wall clock time: 41 minutes 24.30 seconds (2484.30 seconds total)