Starting phenix.real_space_refine
on Sun Apr 27 14:30:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jaq_61300/04_2025/9jaq_61300.cif"
  }
  resolution = 2.99
  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=   0.094
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      46      5.16       5
     C    3886      2.51       5
     N     970      2.21       5
     O    1096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5998
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2999
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 9, 'TRANS': 358}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2999
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 9, 'TRANS': 358}
          Chain breaks: 1
  Time building chain proxies: 4.07, per 1000 atoms: 0.68
  Number of scatterers: 5998
  At special positions: 0
  Unit cell: (118.976, 69.056, 84.032, 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      46     16.00
     O    1096      8.00
     N     970      7.00
     C    3886      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  43 " - pdb=" SG  CYS B  62 " 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 874.1 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      56.0% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 28
      removed outlier: 4.606A  pdb=" N   THR A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ASN A  19 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 39
    Processing helix  chain 'A' and resid 44 through 51
    Processing helix  chain 'A' and resid 64 through 74
    Processing helix  chain 'A' and resid 84 through 100
      removed outlier: 3.879A  pdb=" N   ASP A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
      removed outlier: 3.509A  pdb=" N   VAL A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 118
    Processing helix  chain 'A' and resid 170 through 183
      removed outlier: 4.007A  pdb=" N   ILE A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 203 through 213
      removed outlier: 5.294A  pdb=" N   PHE A 207 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP A 208 " --> pdb=" O   HIS A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 226
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 293 through 310
      removed outlier: 5.175A  pdb=" N   ASP A 297 " --> pdb=" O   ASN A 293 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   ILE A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASP A 299 " --> pdb=" O   ASN A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 6.331A  pdb=" N   GLY A 329 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   MET A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 359
      removed outlier: 3.547A  pdb=" N   LEU A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 372
      removed outlier: 3.770A  pdb=" N   SER A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 417
    Processing helix  chain 'B' and resid 14 through 28
      removed outlier: 4.606A  pdb=" N   THR B  18 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASN B  19 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 39
    Processing helix  chain 'B' and resid 44 through 51
    Processing helix  chain 'B' and resid 64 through 74
    Processing helix  chain 'B' and resid 84 through 100
      removed outlier: 3.881A  pdb=" N   ASP B  94 " --> pdb=" O   LYS B  90 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU B  95 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 108
      removed outlier: 3.509A  pdb=" N   VAL B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 170 through 183
      removed outlier: 4.006A  pdb=" N   ILE B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 213
      removed outlier: 5.292A  pdb=" N   PHE B 207 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ASP B 208 " --> pdb=" O   HIS B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 226
    Processing helix  chain 'B' and resid 264 through 266
      No H-bonds generated for 'chain 'B' and resid 264 through 266'
    Processing helix  chain 'B' and resid 293 through 310
      removed outlier: 5.174A  pdb=" N   ASP B 297 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   ILE B 298 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP B 299 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 342
      removed outlier: 6.332A  pdb=" N   GLY B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   MET B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 359
      removed outlier: 3.547A  pdb=" N   LEU B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL B 353 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE B 357 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE B 359 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 372
      removed outlier: 3.769A  pdb=" N   SER B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 372
      removed outlier: 3.769A  pdb=" N   SER B 370 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 187 through 189
    current: chain 'A' and resid 192 through 194
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 192 through 194
    current: chain 'A' and resid 231 through 238
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 231 through 238
    current: chain 'A' and resid 241 through 248
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 241 through 248
    current: chain 'A' and resid 253 through 257
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 253 through 257
    current: chain 'A' and resid 273 through 277
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 273 through 277
    current: chain 'A' and resid 281 through 283
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 189
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 187 through 189
    current: chain 'B' and resid 192 through 194
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 192 through 194
    current: chain 'B' and resid 231 through 238
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 231 through 238
    current: chain 'B' and resid 241 through 248
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 241 through 248
    current: chain 'B' and resid 253 through 257
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 253 through 257
    current: chain 'B' and resid 273 through 277
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 273 through 277
    current: chain 'B' and resid 281 through 283
  No H-bonds generated for sheet with id=AA2

    244 hydrogen bonds defined for protein.
    708 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: 1.48

  Time building geometry restraints manager: 1.75 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: 1844
        1.34 -     1.46: 1557
        1.46 -     1.58: 2675
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6142
  Sorted by residual:
  bond pdb=" C   ILE B  12 "
       pdb=" N   PRO B  13 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.18e+00
  bond pdb=" CG  LEU A 338 "
       pdb=" CD1 LEU A 338 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" CB  GLN B 180 "
       pdb=" CG  GLN B 180 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" C   ILE A  12 "
       pdb=" N   PRO A  13 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  bond pdb=" N   GLU A  91 "
       pdb=" CA  GLU A  91 "
    ideal  model  delta    sigma   weight residual
    1.456  1.470 -0.014 1.33e-02 5.65e+03 1.08e+00
  ... (remaining 6137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 7992
        1.53 -     3.05: 257
        3.05 -     4.58: 18
        4.58 -     6.11: 5
        6.11 -     7.63: 2
  Bond angle restraints: 8274
  Sorted by residual:
  angle pdb=" N   GLU B 325 "
        pdb=" CA  GLU B 325 "
        pdb=" C   GLU B 325 "
      ideal   model   delta    sigma   weight residual
     110.80  118.43   -7.63 2.13e+00 2.20e-01 1.28e+01
  angle pdb=" N   GLU A 325 "
        pdb=" CA  GLU A 325 "
        pdb=" C   GLU A 325 "
      ideal   model   delta    sigma   weight residual
     110.80  118.30   -7.50 2.13e+00 2.20e-01 1.24e+01
  angle pdb=" C   SER B 289 "
        pdb=" N   VAL B 290 "
        pdb=" CA  VAL B 290 "
      ideal   model   delta    sigma   weight residual
     121.97  118.10    3.87 1.80e+00 3.09e-01 4.63e+00
  angle pdb=" N   GLU B  91 "
        pdb=" CA  GLU B  91 "
        pdb=" C   GLU B  91 "
      ideal   model   delta    sigma   weight residual
     113.28  110.69    2.59 1.22e+00 6.72e-01 4.52e+00
  angle pdb=" C   SER A 289 "
        pdb=" N   VAL A 290 "
        pdb=" CA  VAL A 290 "
      ideal   model   delta    sigma   weight residual
     121.97  118.20    3.77 1.80e+00 3.09e-01 4.39e+00
  ... (remaining 8269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 3216
       16.33 -    32.66: 352
       32.66 -    48.99: 64
       48.99 -    65.32: 12
       65.32 -    81.64: 10
  Dihedral angle restraints: 3654
    sinusoidal: 1482
      harmonic: 2172
  Sorted by residual:
  dihedral pdb=" CA  LYS A  59 "
           pdb=" C   LYS A  59 "
           pdb=" N   VAL A  60 "
           pdb=" CA  VAL A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.74  -21.26     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LYS B  59 "
           pdb=" C   LYS B  59 "
           pdb=" N   VAL B  60 "
           pdb=" CA  VAL B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.83  -21.17     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  ASP B 248 "
           pdb=" C   ASP B 248 "
           pdb=" N   LYS B 249 "
           pdb=" CA  LYS B 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 3651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 652
       0.043 -    0.086: 232
       0.086 -    0.129: 15
       0.129 -    0.172: 7
       0.172 -    0.214: 2
  Chirality restraints: 908
  Sorted by residual:
  chirality pdb=" CA  GLU B 325 "
            pdb=" N   GLU B 325 "
            pdb=" C   GLU B 325 "
            pdb=" CB  GLU B 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  GLU A 325 "
            pdb=" N   GLU A 325 "
            pdb=" C   GLU A 325 "
            pdb=" CB  GLU A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CB  ILE B 246 "
            pdb=" CA  ILE B 246 "
            pdb=" CG1 ILE B 246 "
            pdb=" CG2 ILE B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 905 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 342 "    0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO A 343 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 343 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 343 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 342 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO B 343 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 343 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 343 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 343 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A 344 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 344 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 344 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 642
        2.74 -     3.28: 6004
        3.28 -     3.82: 9736
        3.82 -     4.36: 12735
        4.36 -     4.90: 21296
  Nonbonded interactions: 50413
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 408 "
            pdb=" OG1 THR A 412 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   CYS B 408 "
            pdb=" OG1 THR B 412 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   LYS A 351 "
            pdb=" OG1 THR A 355 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   LYS B 351 "
            pdb=" OG1 THR B 355 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   ALA A 182 "
            pdb=" OG  SER A 185 "
     model   vdw
     2.245 3.040
  ... (remaining 50408 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.510
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.490
  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:12.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
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      :  0.005   0.036   6144  Z= 0.221
  Angle     :  0.625   7.632   8278  Z= 0.365
  Chirality :  0.041   0.214    908
  Planarity :  0.004   0.045   1032
  Dihedral  : 14.517  81.644   2244
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.69 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.89 %
    Favored  : 92.82 %
  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: -3.44 (0.25), residues: 728
  helix: -1.75 (0.22), residues: 358
  sheet: -3.16 (0.48), residues: 72
  loop : -2.58 (0.29), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 399 
 HIS   0.003   0.001   HIS A 269 
 PHE   0.012   0.002   PHE A 335 
 TYR   0.009   0.001   TYR A 189 
 ARG   0.002   0.000   ARG A  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11490 (  238)
  hydrogen bonds       : angle       6.54584 (  708)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       3.23657 (    4)
  covalent geometry    : bond        0.00502 ( 6142)
  covalent geometry    : angle       0.62158 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.716 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 146
  average time/residue: 1.3265
  time to fit residues: 201.8019
Evaluate side-chains
  96 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0170
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
A 262 ASN
A 268 HIS
A 295 ASN
B 180 GLN
B 262 ASN
B 295 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.202688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.158173 restraints weight = 6032.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 3.23
r_work: 0.3558 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6144  Z= 0.127
  Angle     :  0.586   9.733   8278  Z= 0.301
  Chirality :  0.039   0.134    908
  Planarity :  0.004   0.036   1032
  Dihedral  :  4.462  14.564    790
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.13 %
    Favored  : 81.09 %
  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: -2.01 (0.29), residues: 728
  helix: -0.28 (0.27), residues: 352
  sheet: -2.59 (0.53), residues: 70
  loop : -2.24 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 399 
 HIS   0.005   0.001   HIS A 268 
 PHE   0.009   0.001   PHE A 193 
 TYR   0.008   0.001   TYR B 189 
 ARG   0.002   0.000   ARG A  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  238)
  hydrogen bonds       : angle       4.82624 (  708)
  SS BOND              : bond        0.00858 (    2)
  SS BOND              : angle       3.48917 (    4)
  covalent geometry    : bond        0.00294 ( 6142)
  covalent geometry    : angle       0.58140 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7623 (mp0)
REVERT: A  171 ASN cc_start: 0.6946 (t0) cc_final: 0.6671 (m-40)
REVERT: A  250 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7026 (tmmm)
REVERT: B   73 GLU cc_start: 0.7763 (mp0) cc_final: 0.7487 (mp0)
REVERT: B  171 ASN cc_start: 0.6900 (t0) cc_final: 0.6651 (m-40)
REVERT: B  211 MET cc_start: 0.5875 (mmm) cc_final: 0.5604 (mmm)
REVERT: B  250 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.6698 (tmmm)
REVERT: B  268 HIS cc_start: 0.7872 (t70) cc_final: 0.7447 (m90)
  outliers start: 19
  outliers final: 4
  residues processed: 107
  average time/residue: 1.2597
  time to fit residues: 141.3879
Evaluate side-chains
  99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  250 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.201082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.157711 restraints weight = 6074.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.90
r_work: 0.3512 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6144  Z= 0.127
  Angle     :  0.541   8.799   8278  Z= 0.283
  Chirality :  0.038   0.129    908
  Planarity :  0.004   0.035   1032
  Dihedral  :  4.316  13.502    790
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 15.69 %
    Favored  : 79.62 %
  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: -1.43 (0.30), residues: 728
  helix:  0.17 (0.28), residues: 354
  sheet: -2.35 (0.56), residues: 70
  loop : -1.91 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 399 
 HIS   0.003   0.001   HIS B 269 
 PHE   0.008   0.001   PHE A 234 
 TYR   0.013   0.001   TYR A 183 
 ARG   0.002   0.000   ARG B 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  238)
  hydrogen bonds       : angle       4.65545 (  708)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       3.26678 (    4)
  covalent geometry    : bond        0.00297 ( 6142)
  covalent geometry    : angle       0.53618 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 96
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8371 (mttp) cc_final: 0.8055 (mptp)
REVERT: A  250 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.6901 (tmmm)
REVERT: A  268 HIS cc_start: 0.7844 (t70) cc_final: 0.7403 (m90)
REVERT: A  303 ARG cc_start: 0.7320 (mtm180) cc_final: 0.6710 (mmm-85)
REVERT: B   73 GLU cc_start: 0.7957 (mp0) cc_final: 0.7610 (mp0)
REVERT: B   90 LYS cc_start: 0.8361 (mttp) cc_final: 0.8049 (mptp)
REVERT: B  250 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.6615 (tmmm)
REVERT: B  268 HIS cc_start: 0.7880 (t70) cc_final: 0.7418 (m90)
REVERT: B  303 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6707 (mmm-85)
  outliers start: 32
  outliers final: 13
  residues processed: 111
  average time/residue: 1.1070
  time to fit residues: 130.3009
Evaluate side-chains
  109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 13 optimal weight:    0.2980
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 269 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.199383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.155753 restraints weight = 6147.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 3.00
r_work: 0.3491 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6144  Z= 0.151
  Angle     :  0.540   8.254   8278  Z= 0.284
  Chirality :  0.039   0.130    908
  Planarity :  0.004   0.037   1032
  Dihedral  :  4.304  14.188    790
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 16.72 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.30), residues: 728
  helix:  0.29 (0.28), residues: 354
  sheet: -2.07 (0.59), residues: 70
  loop : -1.70 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 399 
 HIS   0.003   0.001   HIS B 269 
 PHE   0.008   0.001   PHE B 234 
 TYR   0.015   0.001   TYR B 183 
 ARG   0.003   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  238)
  hydrogen bonds       : angle       4.63808 (  708)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       3.15833 (    4)
  covalent geometry    : bond        0.00355 ( 6142)
  covalent geometry    : angle       0.53592 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7666 (mp0)
REVERT: A  250 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.6892 (tmmm)
REVERT: A  268 HIS cc_start: 0.7876 (t70) cc_final: 0.7349 (m90)
REVERT: A  303 ARG cc_start: 0.7431 (mtm180) cc_final: 0.6797 (mmm-85)
REVERT: B   73 GLU cc_start: 0.8048 (mp0) cc_final: 0.7635 (mp0)
REVERT: B   90 LYS cc_start: 0.8342 (mttp) cc_final: 0.8088 (mptp)
REVERT: B  211 MET cc_start: 0.5831 (mmm) cc_final: 0.5555 (mmm)
REVERT: B  250 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.6650 (tmmm)
REVERT: B  268 HIS cc_start: 0.7886 (t70) cc_final: 0.7364 (m90)
REVERT: B  303 ARG cc_start: 0.7373 (mtm180) cc_final: 0.6783 (mmm-85)
  outliers start: 28
  outliers final: 14
  residues processed: 117
  average time/residue: 0.9732
  time to fit residues: 120.4490
Evaluate side-chains
  110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
B 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.200804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.156461 restraints weight = 6074.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 3.11
r_work: 0.3562 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.003   0.029   6144  Z= 0.134
  Angle     :  0.542   9.981   8278  Z= 0.279
  Chirality :  0.039   0.130    908
  Planarity :  0.004   0.036   1032
  Dihedral  :  4.250  13.909    790
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.18 %
    Favored  : 77.42 %
  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: -0.95 (0.30), residues: 728
  helix:  0.37 (0.28), residues: 356
  sheet: -1.83 (0.62), residues: 70
  loop : -1.49 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 399 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.007   0.001   PHE B 234 
 TYR   0.016   0.001   TYR B 183 
 ARG   0.004   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  238)
  hydrogen bonds       : angle       4.59116 (  708)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       2.99611 (    4)
  covalent geometry    : bond        0.00316 ( 6142)
  covalent geometry    : angle       0.53765 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7702 (mp0)
REVERT: A   90 LYS cc_start: 0.8389 (mttp) cc_final: 0.8073 (mptp)
REVERT: A  250 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.6920 (tmmm)
REVERT: A  303 ARG cc_start: 0.7412 (mtm180) cc_final: 0.6869 (mmm-85)
REVERT: B   73 GLU cc_start: 0.8079 (mp0) cc_final: 0.7623 (mp0)
REVERT: B  196 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6763 (ptt-90)
REVERT: B  211 MET cc_start: 0.5901 (mmm) cc_final: 0.5627 (mmm)
REVERT: B  250 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.6666 (tmmm)
REVERT: B  303 ARG cc_start: 0.7425 (mtm180) cc_final: 0.6852 (mmm-85)
  outliers start: 30
  outliers final: 13
  residues processed: 117
  average time/residue: 0.9742
  time to fit residues: 120.5687
Evaluate side-chains
  109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  196 ARG
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0770
   chunk 56 optimal weight:    0.1980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 ASN
** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.202910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.159678 restraints weight = 5931.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 2.94
r_work: 0.3586 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6144  Z= 0.115
  Angle     :  0.549  10.301   8278  Z= 0.279
  Chirality :  0.039   0.176    908
  Planarity :  0.004   0.033   1032
  Dihedral  :  4.152  16.693    790
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.79 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.31), residues: 728
  helix:  0.54 (0.28), residues: 356
  sheet: -1.67 (0.63), residues: 70
  loop : -1.44 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 399 
 HIS   0.003   0.001   HIS B 241 
 PHE   0.007   0.001   PHE B 234 
 TYR   0.015   0.001   TYR B 183 
 ARG   0.005   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  238)
  hydrogen bonds       : angle       4.52787 (  708)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       2.95296 (    4)
  covalent geometry    : bond        0.00264 ( 6142)
  covalent geometry    : angle       0.54491 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7711 (mp0)
REVERT: A   90 LYS cc_start: 0.8345 (mttp) cc_final: 0.8121 (mptp)
REVERT: A  250 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.6969 (tmmm)
REVERT: A  303 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6898 (mmm-85)
REVERT: A  391 LYS cc_start: 0.7700 (mptt) cc_final: 0.7394 (mptt)
REVERT: B   73 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7699 (mp0)
REVERT: B  211 MET cc_start: 0.5899 (mmm) cc_final: 0.5474 (mmm)
REVERT: B  303 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6885 (mmm-85)
REVERT: B  391 LYS cc_start: 0.7682 (mptt) cc_final: 0.7377 (mptt)
  outliers start: 24
  outliers final: 13
  residues processed: 112
  average time/residue: 0.9995
  time to fit residues: 118.4408
Evaluate side-chains
  112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    0.1980
   chunk 11 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.202128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.157005 restraints weight = 5984.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 3.18
r_work: 0.3509 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6144  Z= 0.136
  Angle     :  0.570   9.170   8278  Z= 0.291
  Chirality :  0.039   0.179    908
  Planarity :  0.004   0.033   1032
  Dihedral  :  4.180  15.508    790
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 20.23 %
    Favored  : 75.51 %
  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: -0.69 (0.31), residues: 728
  helix:  0.55 (0.28), residues: 354
  sheet: -1.64 (0.64), residues: 70
  loop : -1.31 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 399 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.031   0.001   PHE B 107 
 TYR   0.016   0.001   TYR B 183 
 ARG   0.005   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  238)
  hydrogen bonds       : angle       4.57345 (  708)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       2.95133 (    4)
  covalent geometry    : bond        0.00316 ( 6142)
  covalent geometry    : angle       0.56671 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 1.474 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7702 (mp0)
REVERT: A   90 LYS cc_start: 0.8231 (mttp) cc_final: 0.7963 (mptp)
REVERT: A  250 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.6947 (tmmm)
REVERT: A  303 ARG cc_start: 0.7440 (mtm180) cc_final: 0.6942 (mtp85)
REVERT: B   73 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7645 (mp0)
REVERT: B   90 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7928 (mttm)
REVERT: B  211 MET cc_start: 0.5906 (mmm) cc_final: 0.5523 (mmm)
REVERT: B  250 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.6857 (tmmm)
REVERT: B  303 ARG cc_start: 0.7463 (mtm180) cc_final: 0.6949 (mtp85)
  outliers start: 29
  outliers final: 14
  residues processed: 115
  average time/residue: 1.2164
  time to fit residues: 148.5169
Evaluate side-chains
  112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0060
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 HIS
** B 322 GLN ** 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 = 0.4297 r_free = 0.4297 target = 0.201018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.157143 restraints weight = 5942.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 2.83
r_work: 0.3549 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6144  Z= 0.134
  Angle     :  0.565   9.162   8278  Z= 0.289
  Chirality :  0.040   0.183    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.178  16.031    790
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.85 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.64 (0.31), residues: 728
  helix:  0.61 (0.28), residues: 354
  sheet: -1.64 (0.64), residues: 70
  loop : -1.30 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 242 
 HIS   0.004   0.001   HIS B 241 
 PHE   0.041   0.001   PHE B 107 
 TYR   0.018   0.001   TYR B 183 
 ARG   0.003   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  238)
  hydrogen bonds       : angle       4.58037 (  708)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       2.90086 (    4)
  covalent geometry    : bond        0.00312 ( 6142)
  covalent geometry    : angle       0.56157 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7698 (mp0)
REVERT: A  250 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7036 (tmmm)
REVERT: A  303 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7049 (mtp85)
REVERT: B   73 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7660 (mp0)
REVERT: B  171 ASN cc_start: 0.6864 (t0) cc_final: 0.6632 (m-40)
REVERT: B  250 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.6856 (tmmm)
REVERT: B  287 ARG cc_start: 0.6959 (mpp-170) cc_final: 0.6546 (mpp-170)
REVERT: B  303 ARG cc_start: 0.7506 (mtm180) cc_final: 0.7036 (mtp85)
  outliers start: 20
  outliers final: 14
  residues processed: 112
  average time/residue: 1.1544
  time to fit residues: 137.4313
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 25 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.202923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.159150 restraints weight = 5971.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.81
r_work: 0.3571 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6144  Z= 0.135
  Angle     :  0.564   9.175   8278  Z= 0.289
  Chirality :  0.040   0.184    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.185  16.156    790
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.85 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.31), residues: 728
  helix:  0.62 (0.27), residues: 354
  sheet: -1.66 (0.63), residues: 70
  loop : -1.29 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 399 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.038   0.001   PHE A 107 
 TYR   0.021   0.001   TYR B 183 
 ARG   0.002   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  238)
  hydrogen bonds       : angle       4.58971 (  708)
  SS BOND              : bond        0.00217 (    2)
  SS BOND              : angle       2.87511 (    4)
  covalent geometry    : bond        0.00315 ( 6142)
  covalent geometry    : angle       0.56090 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7666 (mp0)
REVERT: A   90 LYS cc_start: 0.8255 (mttp) cc_final: 0.7962 (mptp)
REVERT: A  250 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7054 (tmmm)
REVERT: A  303 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7090 (mtp85)
REVERT: B   73 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7654 (mp0)
REVERT: B  211 MET cc_start: 0.5867 (mmm) cc_final: 0.5618 (mmm)
REVERT: B  250 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.6864 (tmmm)
REVERT: B  303 ARG cc_start: 0.7556 (mtm180) cc_final: 0.7088 (mtp85)
  outliers start: 20
  outliers final: 14
  residues processed: 106
  average time/residue: 1.1402
  time to fit residues: 128.4287
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 43 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** 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 = 0.4298 r_free = 0.4298 target = 0.200883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.146382 restraints weight = 6006.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.43
r_work: 0.3581 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6144  Z= 0.141
  Angle     :  0.577   9.349   8278  Z= 0.296
  Chirality :  0.040   0.196    908
  Planarity :  0.004   0.034   1032
  Dihedral  :  4.205  16.413    790
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.99 %
    Favored  : 75.37 %
  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: -0.60 (0.31), residues: 728
  helix:  0.65 (0.27), residues: 354
  sheet: -1.66 (0.63), residues: 70
  loop : -1.28 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 242 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.031   0.001   PHE B 107 
 TYR   0.020   0.001   TYR B 183 
 ARG   0.002   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  238)
  hydrogen bonds       : angle       4.64667 (  708)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       2.82868 (    4)
  covalent geometry    : bond        0.00332 ( 6142)
  covalent geometry    : angle       0.57332 ( 8274)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 1.695 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7666 (mp0)
REVERT: A   90 LYS cc_start: 0.8252 (mttp) cc_final: 0.7977 (mptp)
REVERT: A  250 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7007 (tmmm)
REVERT: A  303 ARG cc_start: 0.7510 (mtm180) cc_final: 0.7081 (mtp85)
REVERT: B   73 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7639 (mp0)
REVERT: B   90 LYS cc_start: 0.8234 (mttp) cc_final: 0.7924 (mptp)
REVERT: B  171 ASN cc_start: 0.6774 (t0) cc_final: 0.6486 (m-40)
REVERT: B  250 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.6848 (tmmm)
REVERT: B  303 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7094 (mtp85)
  outliers start: 18
  outliers final: 14
  residues processed: 107
  average time/residue: 0.9698
  time to fit residues: 110.0248
Evaluate side-chains
  113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   43 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.202296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.158654 restraints weight = 6087.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.83
r_work: 0.3496 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6144  Z= 0.153
  Angle     :  0.587   9.277   8278  Z= 0.301
  Chirality :  0.040   0.190    908
  Planarity :  0.004   0.036   1032
  Dihedral  :  4.255  15.970    790
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.11 %
    Favored  : 75.51 %
  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: -0.64 (0.31), residues: 728
  helix:  0.61 (0.27), residues: 354
  sheet: -1.71 (0.62), residues: 70
  loop : -1.28 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 399 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.028   0.001   PHE B 107 
 TYR   0.017   0.001   TYR B 183 
 ARG   0.002   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  238)
  hydrogen bonds       : angle       4.64837 (  708)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       2.81103 (    4)
  covalent geometry    : bond        0.00361 ( 6142)
  covalent geometry    : angle       0.58383 ( 8274)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4678.89 seconds
wall clock time: 82 minutes 13.38 seconds (4933.38 seconds total)