Starting phenix.real_space_refine
on Wed Sep 17 06:15:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jaq_61300/09_2025/9jaq_61300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jaq_61300/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jaq_61300/09_2025/9jaq_61300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jaq_61300/09_2025/9jaq_61300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jaq_61300/09_2025/9jaq_61300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jaq_61300/09_2025/9jaq_61300.map"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.094
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.27
  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: 0.53
  Conformation dependent library (CDL) restraints added in 229.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.20
  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: 0.85

  Time building geometry restraints manager: 0.70 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.590
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.480
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A  99 
 TYR   0.009   0.001   TYR A 189 
 PHE   0.012   0.002   PHE A 335 
 TRP   0.010   0.001   TRP A 399 
 HIS   0.003   0.001   HIS A 269 

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

*********************** 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  : 0.222 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 146
  average time/residue: 0.6510
  time to fit residues: 98.8281
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  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN
A 268 HIS
A 295 ASN
A 374 ASN
** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 262 ASN
B 295 ASN
B 374 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.200704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.157391 restraints weight = 6137.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.90
r_work: 0.3542 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6144  Z= 0.150
  Angle     :  0.608  10.698   8278  Z= 0.311
  Chirality :  0.040   0.136    908
  Planarity :  0.004   0.039   1032
  Dihedral  :  4.535  14.121    790
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.28 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.29), residues: 728
  helix: -0.34 (0.27), residues: 350
  sheet: -2.59 (0.53), residues: 70
  loop : -2.13 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 124 
 TYR   0.010   0.001   TYR B 189 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.008   0.001   TRP B 399 
 HIS   0.005   0.001   HIS A 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6142)
  covalent geometry    : angle       0.60353 ( 8274)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       3.49525 (    4)
  hydrogen bonds       : bond        0.04250 (  238)
  hydrogen bonds       : angle       4.87849 (  708)

*********************** 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
  124 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7597 (mp0)
REVERT: A  171 ASN cc_start: 0.6950 (t0) cc_final: 0.6715 (m-40)
REVERT: A  250 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7052 (tmmm)
REVERT: B   73 GLU cc_start: 0.7814 (mp0) cc_final: 0.7556 (mp0)
REVERT: B  171 ASN cc_start: 0.6938 (t0) cc_final: 0.6726 (m-40)
REVERT: B  250 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.6730 (tmmm)
REVERT: B  268 HIS cc_start: 0.7931 (t70) cc_final: 0.7502 (m90)
  outliers start: 25
  outliers final: 9
  residues processed: 110
  average time/residue: 0.5182
  time to fit residues: 59.8182
Evaluate side-chains
  106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  250 LYS
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0970
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 18 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
B 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.203747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.160101 restraints weight = 6021.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 3.09
r_work: 0.3613 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6144  Z= 0.106
  Angle     :  0.518   7.989   8278  Z= 0.271
  Chirality :  0.038   0.129    908
  Planarity :  0.004   0.035   1032
  Dihedral  :  4.216  12.296    790
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.86 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.30), residues: 728
  helix:  0.31 (0.28), residues: 356
  sheet: -2.23 (0.57), residues: 70
  loop : -1.82 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.007   0.001   PHE A 193 
 TRP   0.004   0.001   TRP A 399 
 HIS   0.002   0.000   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6142)
  covalent geometry    : angle       0.51243 ( 8274)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       3.38930 (    4)
  hydrogen bonds       : bond        0.03787 (  238)
  hydrogen bonds       : angle       4.56072 (  708)

*********************** 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
  126 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8255 (mttp) cc_final: 0.7980 (mptp)
REVERT: A  268 HIS cc_start: 0.7827 (t70) cc_final: 0.7348 (m90)
REVERT: A  303 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6721 (mmm-85)
REVERT: B   73 GLU cc_start: 0.8002 (mp0) cc_final: 0.7662 (mp0)
REVERT: B   90 LYS cc_start: 0.8237 (mttp) cc_final: 0.7998 (mptp)
REVERT: B  250 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.6565 (tmmm)
REVERT: B  268 HIS cc_start: 0.7838 (t70) cc_final: 0.7342 (m90)
REVERT: B  303 ARG cc_start: 0.7320 (mtm180) cc_final: 0.6711 (mmm-85)
  outliers start: 23
  outliers final: 8
  residues processed: 114
  average time/residue: 0.4769
  time to fit residues: 57.4073
Evaluate side-chains
  100 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  232 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  232 VAL
Chi-restraints excluded: chain B residue  250 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0980
   chunk 16 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4314 r_free = 0.4314 target = 0.202494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.159176 restraints weight = 6000.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 3.12
r_work: 0.3525 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6144  Z= 0.114
  Angle     :  0.524   8.371   8278  Z= 0.269
  Chirality :  0.038   0.127    908
  Planarity :  0.004   0.034   1032
  Dihedral  :  4.123  13.650    790
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.45 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.31), residues: 728
  helix:  0.48 (0.28), residues: 356
  sheet: -1.90 (0.60), residues: 70
  loop : -1.63 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 287 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.006   0.001   PHE A 234 
 TRP   0.006   0.001   TRP B 399 
 HIS   0.002   0.000   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6142)
  covalent geometry    : angle       0.51952 ( 8274)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       3.07642 (    4)
  hydrogen bonds       : bond        0.03807 (  238)
  hydrogen bonds       : angle       4.48646 (  708)

*********************** 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
  126 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7655 (mp0)
REVERT: A   90 LYS cc_start: 0.8277 (mttp) cc_final: 0.8048 (mptp)
REVERT: A  250 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.6872 (tmmm)
REVERT: A  268 HIS cc_start: 0.7807 (t70) cc_final: 0.7384 (m90)
REVERT: A  303 ARG cc_start: 0.7369 (mtm180) cc_final: 0.6791 (mmm-85)
REVERT: B   73 GLU cc_start: 0.8053 (mp0) cc_final: 0.7642 (mp0)
REVERT: B   90 LYS cc_start: 0.8269 (mttp) cc_final: 0.8001 (mptp)
REVERT: B  250 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.6511 (tmmm)
REVERT: B  268 HIS cc_start: 0.7819 (t70) cc_final: 0.7378 (m90)
REVERT: B  287 ARG cc_start: 0.6688 (mpp-170) cc_final: 0.6431 (mpp-170)
REVERT: B  303 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6787 (mmm-85)
  outliers start: 26
  outliers final: 12
  residues processed: 113
  average time/residue: 0.4406
  time to fit residues: 52.7100
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  : 0.239 
-------------------------------------------------------------------------------
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  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  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 14 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4294 r_free = 0.4294 target = 0.200454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.156539 restraints weight = 6139.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 3.03
r_work: 0.3495 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2587

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= 0.142
  Angle     :  0.546   8.288   8278  Z= 0.283
  Chirality :  0.039   0.137    908
  Planarity :  0.004   0.035   1032
  Dihedral  :  4.201  15.646    790
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 17.60 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.31), residues: 728
  helix:  0.48 (0.28), residues: 356
  sheet: -1.77 (0.62), residues: 70
  loop : -1.48 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 287 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.008   0.001   PHE B 234 
 TRP   0.007   0.001   TRP A 399 
 HIS   0.003   0.001   HIS B 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6142)
  covalent geometry    : angle       0.54254 ( 8274)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       3.00155 (    4)
  hydrogen bonds       : bond        0.04013 (  238)
  hydrogen bonds       : angle       4.55556 (  708)

*********************** 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
  132 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (mp0)
REVERT: A  250 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.6920 (tmmm)
REVERT: A  268 HIS cc_start: 0.7821 (t70) cc_final: 0.7364 (m90)
REVERT: A  303 ARG cc_start: 0.7411 (mtm180) cc_final: 0.6847 (mmm-85)
REVERT: B   73 GLU cc_start: 0.8103 (mp0) cc_final: 0.7652 (mp0)
REVERT: B  171 ASN cc_start: 0.6919 (t0) cc_final: 0.6684 (m-40)
REVERT: B  211 MET cc_start: 0.5768 (mmm) cc_final: 0.5542 (mmm)
REVERT: B  250 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.6585 (tmmm)
REVERT: B  268 HIS cc_start: 0.7865 (t70) cc_final: 0.7343 (m90)
REVERT: B  303 ARG cc_start: 0.7426 (mtm180) cc_final: 0.6848 (mmm-85)
  outliers start: 29
  outliers final: 15
  residues processed: 119
  average time/residue: 0.4887
  time to fit residues: 61.2363
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  : 0.293 
-------------------------------------------------------------------------------
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  291 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.200920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.156447 restraints weight = 6012.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 3.14
r_work: 0.3484 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2765

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= 0.144
  Angle     :  0.552   9.574   8278  Z= 0.284
  Chirality :  0.039   0.130    908
  Planarity :  0.004   0.035   1032
  Dihedral  :  4.223  15.355    790
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.33 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.31), residues: 728
  helix:  0.48 (0.28), residues: 356
  sheet: -1.70 (0.63), residues: 70
  loop : -1.42 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 287 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.008   0.001   PHE B 234 
 TRP   0.006   0.001   TRP A 399 
 HIS   0.003   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6142)
  covalent geometry    : angle       0.54784 ( 8274)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       2.97344 (    4)
  hydrogen bonds       : bond        0.03984 (  238)
  hydrogen bonds       : angle       4.59358 (  708)

*********************** 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
  133 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7714 (mp0)
REVERT: A  250 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.6949 (tmmm)
REVERT: A  287 ARG cc_start: 0.6783 (mpp-170) cc_final: 0.6546 (mpp-170)
REVERT: A  303 ARG cc_start: 0.7445 (mtm180) cc_final: 0.6936 (mtp85)
REVERT: B   73 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7668 (mp0)
REVERT: B   90 LYS cc_start: 0.8325 (mttp) cc_final: 0.8057 (mptp)
REVERT: B  211 MET cc_start: 0.5832 (mmm) cc_final: 0.5444 (mmm)
REVERT: B  250 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.6624 (tmmm)
REVERT: B  303 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6904 (mmm-85)
  outliers start: 30
  outliers final: 11
  residues processed: 119
  average time/residue: 0.4774
  time to fit residues: 59.7698
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  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
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   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  320 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0570
   chunk 57 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.4898

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.203758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.159671 restraints weight = 6002.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 3.08
r_work: 0.3599 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2889

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= 0.120
  Angle     :  0.570  11.107   8278  Z= 0.289
  Chirality :  0.040   0.244    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.136  16.149    790
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.67 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.31), residues: 728
  helix:  0.65 (0.28), residues: 354
  sheet: -1.57 (0.63), residues: 70
  loop : -1.25 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 287 
 TYR   0.015   0.001   TYR B 183 
 PHE   0.032   0.001   PHE B 107 
 TRP   0.004   0.001   TRP A 242 
 HIS   0.003   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6142)
  covalent geometry    : angle       0.56621 ( 8274)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       2.94365 (    4)
  hydrogen bonds       : bond        0.03764 (  238)
  hydrogen bonds       : angle       4.53057 (  708)

*********************** 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
  123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7701 (mp0)
REVERT: A   90 LYS cc_start: 0.8226 (mttp) cc_final: 0.7940 (mptp)
REVERT: A  250 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7022 (tmmm)
REVERT: A  287 ARG cc_start: 0.6782 (mpp-170) cc_final: 0.6503 (mpp-170)
REVERT: A  303 ARG cc_start: 0.7430 (mtm180) cc_final: 0.6951 (mtp85)
REVERT: B   73 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7660 (mp0)
REVERT: B   90 LYS cc_start: 0.8230 (mttp) cc_final: 0.7964 (mptp)
REVERT: B  211 MET cc_start: 0.5897 (mmm) cc_final: 0.5515 (mmm)
REVERT: B  303 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7003 (mtp85)
  outliers start: 23
  outliers final: 15
  residues processed: 112
  average time/residue: 0.4810
  time to fit residues: 56.8057
Evaluate side-chains
  116 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  214 HIS
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  214 HIS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.201114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.157540 restraints weight = 6018.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 2.82
r_work: 0.3554 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2985

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= 0.138
  Angle     :  0.580  10.587   8278  Z= 0.295
  Chirality :  0.041   0.273    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.181  16.460    790
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.31), residues: 728
  helix:  0.64 (0.28), residues: 354
  sheet: -1.60 (0.63), residues: 70
  loop : -1.25 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 287 
 TYR   0.018   0.001   TYR B 183 
 PHE   0.042   0.001   PHE B 107 
 TRP   0.006   0.001   TRP B 399 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6142)
  covalent geometry    : angle       0.57612 ( 8274)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       2.91114 (    4)
  hydrogen bonds       : bond        0.03949 (  238)
  hydrogen bonds       : angle       4.56877 (  708)

*********************** 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
  123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7692 (mp0)
REVERT: A  250 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7009 (tmmm)
REVERT: A  303 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7069 (mtp85)
REVERT: A  391 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7318 (mptt)
REVERT: B   73 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7640 (mp0)
REVERT: B   90 LYS cc_start: 0.8200 (mttp) cc_final: 0.7915 (mptp)
REVERT: B  171 ASN cc_start: 0.6829 (t0) cc_final: 0.6528 (m-40)
REVERT: B  211 MET cc_start: 0.5924 (mmm) cc_final: 0.5570 (mmm)
REVERT: B  303 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7053 (mtp85)
  outliers start: 23
  outliers final: 13
  residues processed: 112
  average time/residue: 0.4800
  time to fit residues: 56.7707
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  320 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 57 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 22 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.202229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158619 restraints weight = 5978.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.83
r_work: 0.3567 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3129

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= 0.130
  Angle     :  0.581  13.537   8278  Z= 0.293
  Chirality :  0.040   0.208    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.123  16.339    790
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.31), residues: 728
  helix:  0.75 (0.28), residues: 354
  sheet: -1.53 (0.63), residues: 70
  loop : -1.26 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 287 
 TYR   0.019   0.001   TYR B 183 
 PHE   0.042   0.001   PHE A 107 
 TRP   0.005   0.001   TRP A 242 
 HIS   0.003   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6142)
  covalent geometry    : angle       0.57806 ( 8274)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       2.88682 (    4)
  hydrogen bonds       : bond        0.03791 (  238)
  hydrogen bonds       : angle       4.56201 (  708)

*********************** 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
  123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7668 (mp0)
REVERT: A  250 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7081 (tmmm)
REVERT: A  287 ARG cc_start: 0.6941 (mpp-170) cc_final: 0.6530 (mpp-170)
REVERT: A  303 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7094 (mtp85)
REVERT: A  391 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7581 (mptt)
REVERT: B   73 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7655 (mp0)
REVERT: B  171 ASN cc_start: 0.6803 (t0) cc_final: 0.6506 (m-40)
REVERT: B  250 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.6847 (tmmm)
REVERT: B  303 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7096 (mtp85)
  outliers start: 21
  outliers final: 13
  residues processed: 112
  average time/residue: 0.5051
  time to fit residues: 59.5871
Evaluate side-chains
  115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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   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 62 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.202054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.158508 restraints weight = 5979.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.77
r_work: 0.3515 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3174

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= 0.149
  Angle     :  0.600  13.456   8278  Z= 0.303
  Chirality :  0.040   0.205    908
  Planarity :  0.004   0.033   1032
  Dihedral  :  4.208  15.762    790
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.70 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.31), residues: 728
  helix:  0.68 (0.28), residues: 354
  sheet: -1.58 (0.62), residues: 70
  loop : -1.27 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 287 
 TYR   0.019   0.001   TYR B 183 
 PHE   0.030   0.001   PHE B 107 
 TRP   0.006   0.001   TRP B 399 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6142)
  covalent geometry    : angle       0.59654 ( 8274)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       2.84305 (    4)
  hydrogen bonds       : bond        0.04042 (  238)
  hydrogen bonds       : angle       4.64659 (  708)

********************** 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
  122 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7660 (mp0)
REVERT: A   90 LYS cc_start: 0.8156 (mttm) cc_final: 0.7950 (mptp)
REVERT: A  250 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7072 (tmmm)
REVERT: A  303 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7111 (mtp85)
REVERT: A  391 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7556 (mptt)
REVERT: B   73 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7644 (mp0)
REVERT: B  211 MET cc_start: 0.5842 (mmm) cc_final: 0.5430 (mmm)
REVERT: B  250 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.6840 (tmmm)
REVERT: B  303 ARG cc_start: 0.7536 (mtm180) cc_final: 0.7102 (mtp85)
  outliers start: 22
  outliers final: 13
  residues processed: 112
  average time/residue: 0.4719
  time to fit residues: 55.7638
Evaluate side-chains
  114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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   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 26 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6782

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.203800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.160434 restraints weight = 5997.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.83
r_work: 0.3514 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3264

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= 0.134
  Angle     :  0.591  13.466   8278  Z= 0.299
  Chirality :  0.040   0.219    908
  Planarity :  0.004   0.032   1032
  Dihedral  :  4.156  15.888    790
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.31), residues: 728
  helix:  0.77 (0.28), residues: 354
  sheet: -1.52 (0.63), residues: 70
  loop : -1.26 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 287 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.026   0.001   PHE B 107 
 TRP   0.005   0.001   TRP A 242 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6142)
  covalent geometry    : angle       0.58821 ( 8274)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       2.87898 (    4)
  hydrogen bonds       : bond        0.03867 (  238)
  hydrogen bonds       : angle       4.58466 (  708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2115.97 seconds
wall clock time: 37 minutes 0.89 seconds (2220.89 seconds total)