Starting phenix.real_space_refine
on Wed Mar 12 08:44:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1r_32947/03_2025/7x1r_32947.cif"
  }
  resolution = 3.9
  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=   0.019
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: 6
    Type Number    sf(0)   Gaussians
     Au      2     10.57       5
     P       4      5.49       5
     S      38      5.16       5
     C    4824      2.51       5
     N    1298      2.21       5
     O    1442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 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: 7608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3750
          Classifications: {'peptide': 485}
          Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {' AU': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1419  SG  CYS A 189      73.629  62.408  61.033  1.00 28.54           S

  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb="AU    AU A 502 " occ=0.30
    residue:
      pdb="AU    AU B 502 " occ=0.30
  Time building chain proxies: 6.62, per 1000 atoms: 0.87
  Number of scatterers: 7608
  At special positions: 0
  Unit cell: (116.8, 104, 76.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Au      2     78.96
     S      38     16.00
     P       4     15.00
     O    1442      8.00
     N    1298      7.00
     C    4824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A  64 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  59 " - pdb=" SG  CYS B  64 " distance=2.04

  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      36.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 4.346A  pdb=" N   VAL A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 123
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 184'
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 342 through 359
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 430 through 432
      No H-bonds generated for 'chain 'A' and resid 430 through 432'
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 452 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 468
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'B' and resid 21 through 34
      removed outlier: 3.679A  pdb=" N   TYR B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 4.347A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 4.127A  pdb=" N   ARG B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 123
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 180 through 184
      removed outlier: 4.188A  pdb=" N   PHE B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 184'
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 229 through 243
    Processing helix  chain 'B' and resid 342 through 359
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 430 through 432
      No H-bonds generated for 'chain 'B' and resid 430 through 432'
    Processing helix  chain 'B' and resid 444 through 458
      removed outlier: 4.208A  pdb=" N   GLY B 451 " --> pdb=" O   GLU B 447 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 468
    Processing helix  chain 'B' and resid 474 through 481
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ARG A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  15 " --> pdb=" O   MET A  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE A  17 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A  14 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   LEU A 158 " --> pdb=" O   ASP A  14 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR A 330 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   PHE A 157 " --> pdb=" O   TYR A 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.828A  pdb=" N   ILE A 178 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN A 272 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ARG A 266 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL A 435 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN A 428 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ARG B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 135 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128
      removed outlier: 7.235A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  15 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B  14 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   LEU B 158 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE B  16 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   TYR B 330 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   PHE B 157 " --> pdb=" O   TYR B 330 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179
      removed outlier: 6.829A  pdb=" N   ILE B 178 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260
      removed outlier: 5.997A  pdb=" N   GLN B 272 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ARG B 266 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374
      removed outlier: 5.929A  pdb=" N   VAL B 435 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASN B 428 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)

    342 hydrogen bonds defined for protein.
    948 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: 2.49

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2486
        1.35 -     1.47: 1858
        1.47 -     1.60: 3368
        1.60 -     1.72: 0
        1.72 -     1.85: 52
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" O3P FAD B 501 "
       pdb=" P   FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" O3P FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.660  1.559  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" O5B FAD A 501 "
       pdb=" PA  FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O5B FAD B 501 "
       pdb=" PA  FAD B 501 "
    ideal  model  delta    sigma   weight residual
    1.634  1.557  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" O5' FAD A 501 "
       pdb=" P   FAD A 501 "
    ideal  model  delta    sigma   weight residual
    1.637  1.573  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 10120
        1.67 -     3.33: 354
        3.33 -     5.00: 33
        5.00 -     6.66: 21
        6.66 -     8.33: 4
  Bond angle restraints: 10532
  Sorted by residual:
  angle pdb=" N   VAL A 305 "
        pdb=" CA  VAL A 305 "
        pdb=" C   VAL A 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" N   VAL B 305 "
        pdb=" CA  VAL B 305 "
        pdb=" C   VAL B 305 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" C   GLY A 207 "
        pdb=" N   PHE A 208 "
        pdb=" CA  PHE A 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.43    5.71 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   GLY B 207 "
        pdb=" N   PHE B 208 "
        pdb=" CA  PHE B 208 "
      ideal   model   delta    sigma   weight residual
     121.14  115.45    5.69 1.75e+00 3.27e-01 1.06e+01
  angle pdb=" C   ARG B 221 "
        pdb=" N   SER B 222 "
        pdb=" CA  SER B 222 "
      ideal   model   delta    sigma   weight residual
     122.17  117.21    4.96 1.54e+00 4.22e-01 1.04e+01
  ... (remaining 10527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4241
       17.52 -    35.03: 327
       35.03 -    52.55: 66
       52.55 -    70.06: 16
       70.06 -    87.58: 16
  Dihedral angle restraints: 4666
    sinusoidal: 1912
      harmonic: 2754
  Sorted by residual:
  dihedral pdb=" CA  CYS A  59 "
           pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.60  -74.60     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  CYS B  59 "
           pdb=" CB  CYS B  59 "
           pdb=" SG  CYS B  59 "
           pdb=" SG  CYS B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.55  -74.55     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  ALA B 160 "
           pdb=" C   ALA B 160 "
           pdb=" N   THR B 161 "
           pdb=" CA  THR B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 653
       0.034 -    0.068: 317
       0.068 -    0.102: 141
       0.102 -    0.136: 54
       0.136 -    0.169: 9
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  PHE B 208 "
            pdb=" N   PHE B 208 "
            pdb=" C   PHE B 208 "
            pdb=" CB  PHE B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  PHE A 208 "
            pdb=" N   PHE A 208 "
            pdb=" C   PHE A 208 "
            pdb=" CB  PHE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" C2B FAD B 501 "
            pdb=" C1B FAD B 501 "
            pdb=" C3B FAD B 501 "
            pdb=" O2B FAD B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.70    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 170 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO B 171 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 171 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 171 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 170 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 171 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 171 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 171 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 208 "    0.011 2.00e-02 2.50e+03   9.59e-03 1.61e+00
        pdb=" CG  PHE B 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 208 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 208 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 208 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 208 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 969
        2.74 -     3.28: 7362
        3.28 -     3.82: 12429
        3.82 -     4.36: 14855
        4.36 -     4.90: 25607
  Nonbonded interactions: 61222
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 189 "
            pdb="AU    AU B 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" SG  CYS A 189 "
            pdb="AU    AU A 502 "
     model   vdw
     2.205 2.980
  nonbonded pdb=" O   LEU A  55 "
            pdb=" ND2 ASN A 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   LEU B  55 "
            pdb=" ND2 ASN B 113 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG1 THR B 324 "
            pdb=" O   ILE B 329 "
     model   vdw
     2.229 3.040
  ... (remaining 61217 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: 0.04
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=0.30 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:             0.120
  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:             0.020
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.340
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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      :  0.007   0.101   7764  Z= 0.473
  Angle     :  0.755   8.330  10532  Z= 0.413
  Chirality :  0.049   0.169   1174
  Planarity :  0.004   0.032   1336
  Dihedral  : 14.250  87.578   2916
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.02 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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: -0.91 (0.24), residues: 966
  helix:  0.38 (0.27), residues: 290
  sheet: -0.35 (0.32), residues: 264
  loop : -1.43 (0.26), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  53 
 HIS   0.005   0.002   HIS A  71 
 PHE   0.022   0.003   PHE B 208 
 TYR   0.015   0.002   TYR B 200 
 ARG   0.003   0.001   ARG A 434 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt)
REVERT: A   30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6698 (mm-30)
REVERT: A   81 GLN cc_start: 0.8038 (tt0) cc_final: 0.7754 (tt0)
REVERT: A   85 ASN cc_start: 0.8588 (m110) cc_final: 0.8295 (m-40)
REVERT: A  139 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7828 (mtp85)
REVERT: A  140 ILE cc_start: 0.8785 (pt) cc_final: 0.8420 (pt)
REVERT: A  222 SER cc_start: 0.8721 (p) cc_final: 0.8229 (t)
REVERT: A  308 LYS cc_start: 0.7830 (mttp) cc_final: 0.7463 (tttm)
REVERT: A  353 LEU cc_start: 0.9041 (tp) cc_final: 0.8723 (tp)
REVERT: A  396 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A  397 GLU cc_start: 0.7205 (pt0) cc_final: 0.6688 (mt-10)
REVERT: A  450 GLN cc_start: 0.8877 (tp40) cc_final: 0.8558 (tp-100)
REVERT: B   44 VAL cc_start: 0.8996 (p) cc_final: 0.8793 (m)
REVERT: B   85 ASN cc_start: 0.8554 (m110) cc_final: 0.8342 (m-40)
REVERT: B   93 THR cc_start: 0.8339 (t) cc_final: 0.8067 (p)
REVERT: B  192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7447 (ttmm)
REVERT: B  222 SER cc_start: 0.8527 (p) cc_final: 0.8124 (t)
REVERT: B  252 VAL cc_start: 0.9111 (p) cc_final: 0.8899 (m)
REVERT: B  308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7443 (tttm)
REVERT: B  396 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: B  397 GLU cc_start: 0.7094 (pt0) cc_final: 0.6768 (mt-10)
REVERT: B  425 ILE cc_start: 0.8846 (pt) cc_final: 0.8392 (mt)
REVERT: B  450 GLN cc_start: 0.8890 (tp40) cc_final: 0.8554 (tp-100)
  outliers start: 2
  outliers final: 2
  residues processed: 276
  average time/residue: 0.2302
  time to fit residues: 81.5186
Evaluate side-chains
  187 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue  370 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.1980
   chunk 72 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0030
   chunk 24 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
B 113 ASN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.141162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.122460 restraints weight = 8825.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.124604 restraints weight = 6328.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.126270 restraints weight = 4985.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7764  Z= 0.202
  Angle     :  0.569   6.558  10532  Z= 0.305
  Chirality :  0.046   0.153   1174
  Planarity :  0.004   0.051   1336
  Dihedral  :  6.449  45.980   1148
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.79 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.22 (0.26), residues: 966
  helix:  1.92 (0.29), residues: 294
  sheet:  0.07 (0.33), residues: 256
  loop : -1.11 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  98 
 HIS   0.006   0.002   HIS B  96 
 PHE   0.026   0.002   PHE B 208 
 TYR   0.016   0.002   TYR B  13 
 ARG   0.004   0.000   ARG B 268 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 205
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.9002 (mt) cc_final: 0.8672 (mt)
REVERT: A  157 PHE cc_start: 0.8534 (m-80) cc_final: 0.8323 (m-10)
REVERT: A  222 SER cc_start: 0.8720 (p) cc_final: 0.8288 (t)
REVERT: A  308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7439 (tttm)
REVERT: A  397 GLU cc_start: 0.7196 (pt0) cc_final: 0.6677 (mt-10)
REVERT: A  450 GLN cc_start: 0.8736 (tp40) cc_final: 0.8502 (tp-100)
REVERT: A  479 PHE cc_start: 0.8663 (m-80) cc_final: 0.8410 (m-80)
REVERT: B   29 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7664 (mttt)
REVERT: B   44 VAL cc_start: 0.9118 (p) cc_final: 0.8903 (m)
REVERT: B  139 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7748 (mtp85)
REVERT: B  150 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7866 (mtmt)
REVERT: B  157 PHE cc_start: 0.8457 (m-80) cc_final: 0.8246 (m-10)
REVERT: B  192 LYS cc_start: 0.7889 (tttt) cc_final: 0.7538 (ttmm)
REVERT: B  222 SER cc_start: 0.8503 (p) cc_final: 0.8133 (t)
REVERT: B  252 VAL cc_start: 0.8877 (p) cc_final: 0.8675 (m)
REVERT: B  308 LYS cc_start: 0.7853 (mttp) cc_final: 0.7408 (tttm)
REVERT: B  386 SER cc_start: 0.8671 (t) cc_final: 0.8265 (p)
REVERT: B  450 GLN cc_start: 0.8734 (tp40) cc_final: 0.8363 (tp-100)
  outliers start: 13
  outliers final: 8
  residues processed: 214
  average time/residue: 0.1898
  time to fit residues: 55.8375
Evaluate side-chains
  187 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 179
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  436 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 63 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
** B 129 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.142049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.123603 restraints weight = 9028.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.125789 restraints weight = 7298.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.126884 restraints weight = 5361.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7764  Z= 0.171
  Angle     :  0.528   6.063  10532  Z= 0.281
  Chirality :  0.045   0.163   1174
  Planarity :  0.004   0.039   1336
  Dihedral  :  6.189  50.149   1148
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.79 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.58 (0.26), residues: 966
  helix:  2.39 (0.30), residues: 292
  sheet:  0.18 (0.32), residues: 256
  loop : -0.95 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 407 
 HIS   0.004   0.001   HIS B 108 
 PHE   0.024   0.002   PHE B 208 
 TYR   0.011   0.001   TYR B  13 
 ARG   0.004   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  139 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7575 (mtp85)
REVERT: A  222 SER cc_start: 0.8846 (p) cc_final: 0.8461 (t)
REVERT: A  308 LYS cc_start: 0.7965 (mttp) cc_final: 0.7406 (tttm)
REVERT: A  397 GLU cc_start: 0.7185 (pt0) cc_final: 0.6878 (mt-10)
REVERT: A  403 HIS cc_start: 0.8641 (p90) cc_final: 0.8304 (p-80)
REVERT: A  479 PHE cc_start: 0.8449 (m-80) cc_final: 0.7998 (m-80)
REVERT: B   15 LEU cc_start: 0.9271 (tp) cc_final: 0.8962 (tt)
REVERT: B   44 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8788 (m)
REVERT: B  139 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7693 (mtp85)
REVERT: B  222 SER cc_start: 0.8795 (p) cc_final: 0.8355 (t)
REVERT: B  252 VAL cc_start: 0.8731 (p) cc_final: 0.8425 (m)
REVERT: B  289 LEU cc_start: 0.8812 (mt) cc_final: 0.8467 (mp)
REVERT: B  308 LYS cc_start: 0.7920 (mttp) cc_final: 0.7459 (tttm)
REVERT: B  386 SER cc_start: 0.8703 (t) cc_final: 0.8283 (p)
REVERT: B  425 ILE cc_start: 0.8492 (pt) cc_final: 0.7947 (mt)
  outliers start: 26
  outliers final: 21
  residues processed: 214
  average time/residue: 0.1990
  time to fit residues: 57.9888
Evaluate side-chains
  200 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN
B 129 ASN
** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.137046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.118985 restraints weight = 9011.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.119198 restraints weight = 8973.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.120212 restraints weight = 7768.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7764  Z= 0.268
  Angle     :  0.576   5.543  10532  Z= 0.303
  Chirality :  0.046   0.143   1174
  Planarity :  0.004   0.034   1336
  Dihedral  :  6.324  51.103   1148
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 18.17 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.62 (0.26), residues: 966
  helix:  2.54 (0.31), residues: 282
  sheet:  0.12 (0.32), residues: 258
  loop : -0.87 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  53 
 HIS   0.006   0.002   HIS B 243 
 PHE   0.019   0.002   PHE B 208 
 TYR   0.013   0.001   TYR A 358 
 ARG   0.004   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 187
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   39 MET cc_start: 0.9029 (ppp) cc_final: 0.8767 (ppp)
REVERT: A  222 SER cc_start: 0.8939 (p) cc_final: 0.8650 (t)
REVERT: A  257 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6936 (mt-10)
REVERT: A  308 LYS cc_start: 0.8055 (mttp) cc_final: 0.7490 (tttm)
REVERT: A  397 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6983 (mt-10)
REVERT: A  403 HIS cc_start: 0.8711 (p90) cc_final: 0.8291 (p90)
REVERT: A  479 PHE cc_start: 0.8648 (m-80) cc_final: 0.8241 (m-80)
REVERT: B  139 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7603 (mtp85)
REVERT: B  222 SER cc_start: 0.8931 (p) cc_final: 0.8543 (t)
REVERT: B  252 VAL cc_start: 0.8700 (p) cc_final: 0.8369 (m)
REVERT: B  287 VAL cc_start: 0.9115 (t) cc_final: 0.8863 (m)
REVERT: B  308 LYS cc_start: 0.8057 (mttp) cc_final: 0.7528 (tttm)
  outliers start: 40
  outliers final: 30
  residues processed: 217
  average time/residue: 0.1771
  time to fit residues: 52.9067
Evaluate side-chains
  203 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 171
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  192 LYS
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  250 GLN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  480 THR
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 68 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   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 243 HIS
B 243 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.141148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.123416 restraints weight = 8873.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.124577 restraints weight = 7695.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.125646 restraints weight = 6163.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7764  Z= 0.159
  Angle     :  0.522   5.706  10532  Z= 0.275
  Chirality :  0.044   0.145   1174
  Planarity :  0.004   0.034   1336
  Dihedral  :  6.181  51.016   1148
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.80 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.91 (0.27), residues: 966
  helix:  2.69 (0.31), residues: 280
  sheet:  0.40 (0.33), residues: 244
  loop : -0.65 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 407 
 HIS   0.005   0.001   HIS B  96 
 PHE   0.025   0.002   PHE B 208 
 TYR   0.010   0.001   TYR A 358 
 ARG   0.005   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   39 MET cc_start: 0.9076 (ppp) cc_final: 0.8840 (ppp)
REVERT: A   76 LEU cc_start: 0.9211 (mp) cc_final: 0.8758 (mm)
REVERT: A   82 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7523 (t0)
REVERT: A  139 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7549 (mtp85)
REVERT: A  222 SER cc_start: 0.8997 (p) cc_final: 0.8756 (t)
REVERT: A  257 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6767 (mt-10)
REVERT: A  308 LYS cc_start: 0.8115 (mttp) cc_final: 0.7514 (tttm)
REVERT: A  397 GLU cc_start: 0.7204 (pt0) cc_final: 0.6983 (mt-10)
REVERT: A  479 PHE cc_start: 0.8496 (m-80) cc_final: 0.8008 (m-80)
REVERT: B   82 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7377 (t0)
REVERT: B  139 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7611 (mtp85)
REVERT: B  222 SER cc_start: 0.8986 (p) cc_final: 0.8635 (t)
REVERT: B  254 ILE cc_start: 0.8754 (pt) cc_final: 0.8419 (mm)
REVERT: B  308 LYS cc_start: 0.8062 (mttp) cc_final: 0.7547 (tttm)
REVERT: B  353 LEU cc_start: 0.8760 (tp) cc_final: 0.8551 (tp)
REVERT: B  403 HIS cc_start: 0.8373 (p90) cc_final: 0.8056 (p90)
  outliers start: 36
  outliers final: 23
  residues processed: 222
  average time/residue: 0.1772
  time to fit residues: 54.8931
Evaluate side-chains
  207 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   82 ASP
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 ASP
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 91 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN
** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.137824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.120114 restraints weight = 8992.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.121407 restraints weight = 6648.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.122260 restraints weight = 5443.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7764  Z= 0.223
  Angle     :  0.556   8.052  10532  Z= 0.290
  Chirality :  0.045   0.155   1174
  Planarity :  0.004   0.035   1336
  Dihedral  :  6.331  51.182   1148
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.80 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.76 (0.27), residues: 966
  helix:  2.49 (0.31), residues: 282
  sheet:  0.30 (0.33), residues: 244
  loop : -0.69 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  88 
 HIS   0.009   0.002   HIS A 243 
 PHE   0.027   0.002   PHE A 208 
 TYR   0.015   0.001   TYR B 284 
 ARG   0.007   0.000   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   39 MET cc_start: 0.9112 (ppp) cc_final: 0.8799 (ppp)
REVERT: A   67 LYS cc_start: 0.9166 (tmmt) cc_final: 0.8870 (ttpt)
REVERT: A   76 LEU cc_start: 0.9286 (mp) cc_final: 0.8942 (mm)
REVERT: A  222 SER cc_start: 0.8979 (p) cc_final: 0.8713 (t)
REVERT: A  257 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6752 (mt-10)
REVERT: A  308 LYS cc_start: 0.8188 (mttp) cc_final: 0.7734 (tttm)
REVERT: A  403 HIS cc_start: 0.8712 (p90) cc_final: 0.8250 (p90)
REVERT: A  479 PHE cc_start: 0.8660 (m-80) cc_final: 0.8278 (m-80)
REVERT: B  101 MET cc_start: 0.8685 (ttp) cc_final: 0.8454 (ttp)
REVERT: B  139 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7620 (mtp85)
REVERT: B  222 SER cc_start: 0.8908 (p) cc_final: 0.8617 (t)
REVERT: B  280 ILE cc_start: 0.7238 (pt) cc_final: 0.6726 (tt)
REVERT: B  289 LEU cc_start: 0.9111 (mt) cc_final: 0.8741 (mp)
REVERT: B  308 LYS cc_start: 0.8190 (mttp) cc_final: 0.7531 (tttm)
REVERT: B  425 ILE cc_start: 0.8478 (pt) cc_final: 0.8235 (mt)
  outliers start: 30
  outliers final: 27
  residues processed: 208
  average time/residue: 0.1889
  time to fit residues: 55.4078
Evaluate side-chains
  210 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  257 GLU
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  245 ILE
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  469 ILE
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 ASN
B 144 ASN
** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.135112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.117826 restraints weight = 9120.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.118962 restraints weight = 6528.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.119547 restraints weight = 5692.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7764  Z= 0.267
  Angle     :  0.588  11.175  10532  Z= 0.307
  Chirality :  0.046   0.150   1174
  Planarity :  0.004   0.042   1336
  Dihedral  :  6.374  50.797   1148
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.81 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    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:  0.59 (0.27), residues: 966
  helix:  2.42 (0.31), residues: 282
  sheet:  0.06 (0.33), residues: 244
  loop : -0.76 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  88 
 HIS   0.005   0.002   HIS B 472 
 PHE   0.024   0.002   PHE B 208 
 TYR   0.012   0.001   TYR B 284 
 ARG   0.009   0.001   ARG B  84 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 188
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   39 MET cc_start: 0.9121 (ppp) cc_final: 0.8796 (ppp)
REVERT: A   67 LYS cc_start: 0.9153 (tmmt) cc_final: 0.8940 (ttpt)
REVERT: A   76 LEU cc_start: 0.9278 (mp) cc_final: 0.9002 (mm)
REVERT: A  140 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8105 (pt)
REVERT: A  163 GLU cc_start: 0.7418 (pt0) cc_final: 0.7090 (pt0)
REVERT: A  222 SER cc_start: 0.9037 (p) cc_final: 0.8751 (t)
REVERT: A  308 LYS cc_start: 0.8120 (mttp) cc_final: 0.7560 (tmtt)
REVERT: A  403 HIS cc_start: 0.8542 (p90) cc_final: 0.8005 (p90)
REVERT: A  479 PHE cc_start: 0.8707 (m-80) cc_final: 0.8430 (m-80)
REVERT: B  139 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7632 (mtp85)
REVERT: B  163 GLU cc_start: 0.7364 (pt0) cc_final: 0.7003 (pt0)
REVERT: B  222 SER cc_start: 0.8892 (p) cc_final: 0.8681 (t)
REVERT: B  280 ILE cc_start: 0.7308 (pt) cc_final: 0.6825 (tt)
REVERT: B  308 LYS cc_start: 0.8147 (mttp) cc_final: 0.7735 (tttm)
REVERT: B  356 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6763 (ttm-80)
REVERT: B  425 ILE cc_start: 0.8534 (pt) cc_final: 0.8266 (mt)
  outliers start: 32
  outliers final: 27
  residues processed: 208
  average time/residue: 0.1669
  time to fit residues: 48.7750
Evaluate side-chains
  211 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  404 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  492 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1014 > 50:
  distance: 71 - 75:  27.162
  distance: 75 - 76:  20.121
  distance: 76 - 77:  40.617
  distance: 76 - 79:  55.860
  distance: 77 - 78:  53.492
  distance: 77 - 84:  39.588
  distance: 79 - 80:  27.312
  distance: 80 - 81:  27.068
  distance: 81 - 82:  23.971
  distance: 81 - 83:  40.307
  distance: 84 - 85:  70.020
  distance: 85 - 86:  28.389
  distance: 85 - 88:  28.726
  distance: 86 - 87:  50.048
  distance: 86 - 92:  13.370
  distance: 88 - 89:  32.205
  distance: 89 - 90:  48.049
  distance: 89 - 91:  14.636
  distance: 92 - 93:  56.888
  distance: 93 - 94:  67.831
  distance: 93 - 96:  40.035
  distance: 94 - 95:  69.965
  distance: 94 - 99:  69.757
  distance: 96 - 97:  42.892
  distance: 96 - 98:  44.264
  distance: 99 - 100:  67.830
  distance: 100 - 101:  12.028
  distance: 100 - 103:  53.098
  distance: 101 - 102:  62.221
  distance: 101 - 106:  59.369
  distance: 103 - 104:  47.392
  distance: 104 - 105:  28.339
  distance: 106 - 182:  30.545
  distance: 107 - 108:  29.384
  distance: 107 - 110:  53.182
  distance: 108 - 109:  37.394
  distance: 108 - 113:  39.843
  distance: 109 - 179:  30.311
  distance: 110 - 111:  39.510
  distance: 110 - 112:   3.279
  distance: 113 - 114:  25.555
  distance: 114 - 115:  32.055
  distance: 114 - 117:  20.734
  distance: 115 - 116:  60.640
  distance: 115 - 120:  44.825
  distance: 117 - 118:  45.002
  distance: 117 - 119:  17.711
  distance: 120 - 121:  49.204
  distance: 120 - 170:  33.132
  distance: 121 - 122:  46.477
  distance: 121 - 124:  48.935
  distance: 122 - 123:  52.017
  distance: 122 - 127:  21.977
  distance: 123 - 167:  37.364
  distance: 124 - 125:  56.853
  distance: 124 - 126:  68.898
  distance: 127 - 128:  30.742
  distance: 128 - 129:  40.081
  distance: 128 - 131:  45.586
  distance: 129 - 130:  55.840
  distance: 129 - 138:  41.259
  distance: 131 - 132:  16.507
  distance: 132 - 133:  39.255
  distance: 132 - 134:   5.149
  distance: 133 - 135:  37.818
  distance: 134 - 136:  53.752
  distance: 135 - 137:  54.635
  distance: 136 - 137:  56.882
  distance: 138 - 139:  39.750
  distance: 140 - 145:  10.924
  distance: 142 - 143:  36.843
  distance: 145 - 146:   8.992
  distance: 145 - 151:  28.745
  distance: 146 - 147:  39.914
  distance: 147 - 152:  35.632
  distance: 149 - 150:  55.635
  distance: 150 - 151:  54.874