Starting phenix.real_space_refine
on Sat May 10 06:41:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r3t_18874/05_2025/8r3t_18874.cif"
  }
  resolution = 3.1
  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=   0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    1644      2.51       5
     N     492      2.21       5
     O     486      1.98       5
     H    2804      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5438
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 906
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
    Chain: "B"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 907
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
    Chain: "C"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 906
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
    Chain: "D"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 906
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
    Chain: "E"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 906
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
    Chain: "F"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 907
          Classifications: {'peptide': 59}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56}
  Time building chain proxies: 3.97, per 1000 atoms: 0.73
  Number of scatterers: 5438
  At special positions: 0
  Unit cell: (66.066, 92.202, 54.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O     486      8.00
     N     492      7.00
     C    1644      6.00
     H    2804      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 322 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 322 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 322 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 322 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 291 " - pdb=" SG  CYS E 322 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 291 " - pdb=" SG  CYS F 322 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 332.1 milliseconds
  

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 55.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 290
      removed outlier: 6.424A  pdb=" N   GLN A 276 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ASN F 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE A 278 " --> pdb=" O   ASN F 279 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   LYS F 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LYS A 280 " --> pdb=" O   LYS F 281 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   ASP F 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LEU A 282 " --> pdb=" O   ASP F 283 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   SER F 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU A 284 " --> pdb=" O   SER F 285 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   VAL F 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ASN A 286 " --> pdb=" O   VAL F 287 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   SER F 289 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLN A 288 " --> pdb=" O   SER F 289 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   CYS F 291 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LYS A 290 " --> pdb=" O   CYS F 291 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS B 274 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   ILE C 277 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   SER C 285 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 284 " --> pdb=" O   SER C 285 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   VAL C 287 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASN B 286 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   SER C 289 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLN B 288 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   CYS C 291 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS B 290 " --> pdb=" O   CYS C 291 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LYS C 274 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   ILE D 277 " --> pdb=" O   LYS C 274 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLN C 276 " --> pdb=" O   ILE D 277 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   ASN D 279 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE C 278 " --> pdb=" O   ASN D 279 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   LYS D 281 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   LYS C 280 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   ASP D 283 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU C 282 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   SER D 285 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU C 284 " --> pdb=" O   SER D 285 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   VAL D 287 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASN C 286 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   SER D 289 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLN C 288 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   CYS D 291 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS C 290 " --> pdb=" O   CYS D 291 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 296
      removed outlier: 6.719A  pdb=" N   ASP A 295 " --> pdb=" O   ASN F 296 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS B 294 " --> pdb=" O   ASP F 295 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASP B 295 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 309
      removed outlier: 6.689A  pdb=" N   SER A 305 " --> pdb=" O   VAL F 306 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ILE F 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   GLN A 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   SER B 305 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   ILE C 308 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 322
      removed outlier: 6.457A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.493A  pdb=" N   CYS F 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LYS A 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   SER C 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   THR B 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   CYS C 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS C 317 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   SER D 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   THR C 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   CYS D 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LYS C 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS D 317 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   SER E 320 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   THR D 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   CYS E 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LYS D 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 330
      removed outlier: 6.021A  pdb=" N   LEU B 325 " --> pdb=" O   GLY F 326 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   ILE F 328 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASN B 327 " --> pdb=" O   ILE F 328 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   HIS F 330 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   HIS B 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    222 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: 1.78

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 2804
        1.12 -     1.30: 432
        1.30 -     1.47: 791
        1.47 -     1.64: 1429
        1.64 -     1.81: 12
  Bond restraints: 5468
  Sorted by residual:
  bond pdb=" N   TYR D 310 "
       pdb=" H   TYR D 310 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   ILE C 278 "
       pdb=" H   ILE C 278 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" N   LYS C 290 "
       pdb=" H   LYS C 290 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" N   TYR C 310 "
       pdb=" H   TYR C 310 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" CD2 HIS F 330 "
       pdb=" HD2 HIS F 330 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.64e+01
  ... (remaining 5463 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 8170
        2.41 -     4.83: 1311
        4.83 -     7.24: 487
        7.24 -     9.65: 30
        9.65 -    12.07: 8
  Bond angle restraints: 10006
  Sorted by residual:
  angle pdb=" C   LYS D 311 "
        pdb=" CA  LYS D 311 "
        pdb=" CB  LYS D 311 "
      ideal   model   delta    sigma   weight residual
     110.17  122.24  -12.07 1.97e+00 2.58e-01 3.75e+01
  angle pdb=" CA  ASP C 295 "
        pdb=" CB  ASP C 295 "
        pdb=" CG  ASP C 295 "
      ideal   model   delta    sigma   weight residual
     112.60  118.63   -6.03 1.00e+00 1.00e+00 3.63e+01
  angle pdb=" CA  ASP F 295 "
        pdb=" CB  ASP F 295 "
        pdb=" CG  ASP F 295 "
      ideal   model   delta    sigma   weight residual
     112.60  118.55   -5.95 1.00e+00 1.00e+00 3.54e+01
  angle pdb=" CA  ASP D 295 "
        pdb=" CB  ASP D 295 "
        pdb=" CG  ASP D 295 "
      ideal   model   delta    sigma   weight residual
     112.60  118.51   -5.91 1.00e+00 1.00e+00 3.49e+01
  angle pdb=" C   LYS B 311 "
        pdb=" CA  LYS B 311 "
        pdb=" CB  LYS B 311 "
      ideal   model   delta    sigma   weight residual
     110.17  121.74  -11.57 1.97e+00 2.58e-01 3.45e+01
  ... (remaining 10001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.09: 2087
       13.09 -    26.17: 240
       26.17 -    39.25: 100
       39.25 -    52.34: 48
       52.34 -    65.42: 47
  Dihedral angle restraints: 2522
    sinusoidal: 1464
      harmonic: 1058
  Sorted by residual:
  dihedral pdb=" CA  LEU C 325 "
           pdb=" C   LEU C 325 "
           pdb=" N   GLY C 326 "
           pdb=" CA  GLY C 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.08  -29.92     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  LEU B 325 "
           pdb=" C   LEU B 325 "
           pdb=" N   GLY B 326 "
           pdb=" CA  GLY B 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.20  -29.80     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" C   LYS B 311 "
           pdb=" N   LYS B 311 "
           pdb=" CA  LYS B 311 "
           pdb=" CB  LYS B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.47   14.87     0      2.50e+00 1.60e-01 3.54e+01
  ... (remaining 2519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 265
       0.088 -    0.177: 114
       0.177 -    0.265: 28
       0.265 -    0.353: 2
       0.353 -    0.442: 5
  Chirality restraints: 414
  Sorted by residual:
  chirality pdb=" CA  LYS B 311 "
            pdb=" N   LYS B 311 "
            pdb=" C   LYS B 311 "
            pdb=" CB  LYS B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.88e+00
  chirality pdb=" CA  LYS E 311 "
            pdb=" N   LYS E 311 "
            pdb=" C   LYS E 311 "
            pdb=" CB  LYS E 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" CA  LYS D 311 "
            pdb=" N   LYS D 311 "
            pdb=" C   LYS D 311 "
            pdb=" CB  LYS D 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.68e+00
  ... (remaining 411 not shown)

  Planarity restraints: 780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 310 "   -0.133 2.00e-02 2.50e+03   6.19e-02 1.15e+02
        pdb=" CG  TYR B 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 310 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 310 "    0.040 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 310 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 310 "   -0.031 2.00e-02 2.50e+03
        pdb=" OH  TYR B 310 "   -0.102 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 310 "    0.093 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 310 "    0.040 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 310 "    0.024 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 310 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 310 "    0.122 2.00e-02 2.50e+03   5.96e-02 1.07e+02
        pdb=" CG  TYR F 310 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 310 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 310 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 310 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 310 "    0.025 2.00e-02 2.50e+03
        pdb=" OH  TYR F 310 "    0.116 2.00e-02 2.50e+03
        pdb=" HD1 TYR F 310 "   -0.056 2.00e-02 2.50e+03
        pdb=" HD2 TYR F 310 "   -0.051 2.00e-02 2.50e+03
        pdb=" HE1 TYR F 310 "   -0.046 2.00e-02 2.50e+03
        pdb=" HE2 TYR F 310 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 310 "    0.108 2.00e-02 2.50e+03   5.12e-02 7.88e+01
        pdb=" CG  TYR C 310 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 310 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 310 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 310 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 310 "    0.020 2.00e-02 2.50e+03
        pdb=" OH  TYR C 310 "    0.097 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 310 "   -0.055 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 310 "   -0.042 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 310 "   -0.032 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 310 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 777 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 577
        2.23 -     2.82: 10474
        2.82 -     3.41: 14060
        3.41 -     4.01: 19022
        4.01 -     4.60: 28200
  Nonbonded interactions: 72333
  Sorted by model distance:
  nonbonded pdb=" HG  SER C 293 "
            pdb=" OD1 ASP C 295 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" HG  SER F 293 "
            pdb=" OD1 ASP F 295 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" HG  SER E 293 "
            pdb=" OD1 ASP E 295 "
     model   vdw
     1.722 2.450
  nonbonded pdb=" OD2 ASP A 295 "
            pdb=" HZ2 LYS F 290 "
     model   vdw
     1.750 2.450
  nonbonded pdb=" HZ1 LYS A 281 "
            pdb=" OD1 ASP A 283 "
     model   vdw
     1.763 2.450
  ... (remaining 72328 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' and (resid 273 through 329 or (resid 330 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ 
 NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ 
e HE1)) or resid 331))
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = (chain 'F' and (resid 273 through 329 or (resid 330 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ 
 NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ 
e HE1)) or resid 331))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.240
  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:             0.090
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.420
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.011   0.039   2670  Z= 0.715
  Angle     :  2.118  12.066   3570  Z= 1.395
  Chirality :  0.106   0.442    414
  Planarity :  0.011   0.060    444
  Dihedral  : 14.975  59.058   1026
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 0.55
  Ramachandran Plot:
    Outliers :  1.75 %
    Allowed  :  2.05 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  :  9.94 %
    Favored  : 84.62 %
  Cbeta Deviations :  1.92 %
  Peptide Plane:
    Cis-proline     : 50.00 %
    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: -1.86 (0.36), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.41 (0.28), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS A 329 
 TYR   0.097   0.038   TYR B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12107 (   74)
  hydrogen bonds       : angle       6.73710 (  222)
  SS BOND              : bond        0.01431 (    6)
  SS BOND              : angle       2.25330 (   12)
  covalent geometry    : bond        0.01112 ( 2664)
  covalent geometry    : angle       2.11717 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 15
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7694 (t0)
REVERT: B  314 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7334 (t0)
REVERT: C  314 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7049 (t0)
REVERT: D  314 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7732 (t70)
REVERT: F  314 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7212 (t0)
  outliers start: 17
  outliers final: 5
  residues processed: 27
  average time/residue: 0.2230
  time to fit residues: 8.0448
Evaluate side-chains
  19 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 9
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  291 CYS
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  322 CYS
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4727 r_free = 0.4727 target = 0.161564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.141695 restraints weight = 8740.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.4566 rms_B_bonded: 2.60
r_work: 0.4477 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.4353 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2670  Z= 0.163
  Angle     :  0.831   7.253   3570  Z= 0.449
  Chirality :  0.056   0.132    414
  Planarity :  0.003   0.023    444
  Dihedral  : 13.115  57.481    369
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  2.34 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  :  9.62 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.70 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B 329 
 TYR   0.008   0.001   TYR A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02866 (   74)
  hydrogen bonds       : angle       5.40689 (  222)
  SS BOND              : bond        0.00111 (    6)
  SS BOND              : angle       1.12904 (   12)
  covalent geometry    : bond        0.00362 ( 2664)
  covalent geometry    : angle       0.82933 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 13
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7474 (t0)
REVERT: B  314 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.6883 (t0)
REVERT: C  314 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6737 (t0)
REVERT: D  314 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7373 (t0)
REVERT: F  314 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6724 (t0)
REVERT: F  322 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6715 (m)
  outliers start: 17
  outliers final: 5
  residues processed: 26
  average time/residue: 0.1553
  time to fit residues: 6.2354
Evaluate side-chains
  20 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 9
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  291 CYS
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain E residue  322 CYS
Chi-restraints excluded: chain E residue  330 HIS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  322 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 296 ASN
C 296 ASN
E 296 ASN
F 296 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.165950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.147563 restraints weight = 8951.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.4543 rms_B_bonded: 2.54
r_work: 0.4428 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.4303 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2670  Z= 0.140
  Angle     :  0.736   6.017   3570  Z= 0.396
  Chirality :  0.055   0.131    414
  Planarity :  0.003   0.028    444
  Dihedral  : 12.499  58.028    368
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  :  8.01 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.81 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.13 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.006   0.001   TYR A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02108 (   74)
  hydrogen bonds       : angle       4.54164 (  222)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.61128 (   12)
  covalent geometry    : bond        0.00300 ( 2664)
  covalent geometry    : angle       0.73161 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 10
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7559 (t0)
REVERT: B  314 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.6978 (t0)
REVERT: C  314 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.6814 (t0)
REVERT: D  314 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7208 (t0)
REVERT: F  314 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.6846 (t0)
REVERT: F  322 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6915 (m)
  outliers start: 16
  outliers final: 4
  residues processed: 21
  average time/residue: 0.1105
  time to fit residues: 4.0980
Evaluate side-chains
  21 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 11
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  322 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 296 ASN
C 296 ASN
E 296 ASN
F 296 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.164262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.145833 restraints weight = 9069.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.4527 rms_B_bonded: 2.55
r_work: 0.4433 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.4319 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2670  Z= 0.157
  Angle     :  0.703   5.698   3570  Z= 0.379
  Chirality :  0.054   0.128    414
  Planarity :  0.003   0.025    444
  Dihedral  : 12.048  59.482    365
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.97 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  :  8.97 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.82 (0.35), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.007   0.002   TYR F 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01701 (   74)
  hydrogen bonds       : angle       4.22397 (  222)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       1.62215 (   12)
  covalent geometry    : bond        0.00340 ( 2664)
  covalent geometry    : angle       0.69738 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 10
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7555 (t0)
REVERT: B  314 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.6908 (t0)
REVERT: C  314 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6679 (t0)
REVERT: D  314 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7156 (t0)
REVERT: F  314 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6732 (t0)
REVERT: F  322 CYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6933 (m)
  outliers start: 14
  outliers final: 2
  residues processed: 19
  average time/residue: 0.1657
  time to fit residues: 4.8542
Evaluate side-chains
  18 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  322 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.155988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.138285 restraints weight = 9509.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.4471 rms_B_bonded: 2.65
r_work: 0.4371 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.4254 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2670  Z= 0.163
  Angle     :  0.697   5.756   3570  Z= 0.376
  Chirality :  0.055   0.133    414
  Planarity :  0.003   0.026    444
  Dihedral  : 11.767  58.990    365
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 12.82 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.79 (0.35), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.27), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.007   0.001   TYR A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01567 (   74)
  hydrogen bonds       : angle       4.29074 (  222)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       1.56348 (   12)
  covalent geometry    : bond        0.00353 ( 2664)
  covalent geometry    : angle       0.69253 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 10
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7509 (t0)
REVERT: B  314 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.6955 (t0)
REVERT: C  314 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.6760 (t0)
REVERT: F  314 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.6669 (t0)
REVERT: F  322 CYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6979 (m)
  outliers start: 11
  outliers final: 2
  residues processed: 16
  average time/residue: 0.1593
  time to fit residues: 3.9807
Evaluate side-chains
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 9
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Chi-restraints excluded: chain F residue  322 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0870
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 ASN ** 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 = 0.4660 r_free = 0.4660 target = 0.159806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.141878 restraints weight = 9422.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.4501 rms_B_bonded: 2.67
r_work: 0.4398 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.4280 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2670  Z= 0.120
  Angle     :  0.641   5.671   3570  Z= 0.343
  Chirality :  0.053   0.129    414
  Planarity :  0.003   0.026    444
  Dihedral  : 11.359  57.183    365
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.10 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -2.84 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 329 
 TYR   0.009   0.002   TYR A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01315 (   74)
  hydrogen bonds       : angle       4.12371 (  222)
  SS BOND              : bond        0.00481 (    6)
  SS BOND              : angle       1.26018 (   12)
  covalent geometry    : bond        0.00262 ( 2664)
  covalent geometry    : angle       0.63839 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 11
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7493 (t0)
REVERT: C  314 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.6821 (t0)
REVERT: F  314 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.6713 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 13
  average time/residue: 0.1974
  time to fit residues: 4.0050
Evaluate side-chains
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 296 ASN
C 296 ASN
E 296 ASN
F 296 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.151205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.131732 restraints weight = 9555.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.4483 rms_B_bonded: 2.57
r_work: 0.4365 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4245 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2670  Z= 0.150
  Angle     :  0.664   5.357   3570  Z= 0.356
  Chirality :  0.054   0.133    414
  Planarity :  0.003   0.026    444
  Dihedral  : 11.404  56.863    365
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.06 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -2.92 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.007   0.001   TYR A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01461 (   74)
  hydrogen bonds       : angle       4.16609 (  222)
  SS BOND              : bond        0.00412 (    6)
  SS BOND              : angle       1.59072 (   12)
  covalent geometry    : bond        0.00333 ( 2664)
  covalent geometry    : angle       0.65863 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 9
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7521 (t0)
REVERT: B  314 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.6987 (t0)
REVERT: C  314 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6731 (t0)
REVERT: F  314 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6833 (t0)
  outliers start: 11
  outliers final: 3
  residues processed: 15
  average time/residue: 0.1749
  time to fit residues: 3.9790
Evaluate side-chains
  17 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 10
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  296 ASN
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 296 ASN
F 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.158877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.140985 restraints weight = 9742.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.4471 rms_B_bonded: 2.62
r_work: 0.4350 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.4225 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2670  Z= 0.153
  Angle     :  0.661   5.350   3570  Z= 0.357
  Chirality :  0.054   0.130    414
  Planarity :  0.003   0.026    444
  Dihedral  : 11.206  57.086    363
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.03 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.95 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.006   0.001   TYR F 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01481 (   74)
  hydrogen bonds       : angle       4.17614 (  222)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       1.58156 (   12)
  covalent geometry    : bond        0.00339 ( 2664)
  covalent geometry    : angle       0.65539 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 10
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7532 (t0)
REVERT: B  314 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7088 (t0)
REVERT: C  314 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.6809 (t0)
REVERT: F  314 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.6871 (t0)
  outliers start: 9
  outliers final: 2
  residues processed: 14
  average time/residue: 0.1805
  time to fit residues: 3.8784
Evaluate side-chains
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.2980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 296 ASN ** 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 = 0.4623 r_free = 0.4623 target = 0.156042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.138846 restraints weight = 9514.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4486 rms_B_bonded: 2.57
r_work: 0.4366 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4241 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2670  Z= 0.129
  Angle     :  0.640   5.490   3570  Z= 0.343
  Chirality :  0.053   0.132    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.003  56.420    363
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.35 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -2.99 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.009   0.002   TYR F 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01342 (   74)
  hydrogen bonds       : angle       4.07127 (  222)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       1.43290 (   12)
  covalent geometry    : bond        0.00290 ( 2664)
  covalent geometry    : angle       0.63593 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7547 (t0)
REVERT: B  314 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7054 (t0)
REVERT: C  314 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.6831 (t0)
REVERT: F  314 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6871 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 12
  average time/residue: 0.2001
  time to fit residues: 3.7628
Evaluate side-chains
  15 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 10
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 296 ASN ** 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 = 0.4663 r_free = 0.4663 target = 0.159487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.142332 restraints weight = 9547.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.4519 rms_B_bonded: 2.54
r_work: 0.4403 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4280 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2670  Z= 0.112
  Angle     :  0.616   5.240   3570  Z= 0.330
  Chirality :  0.053   0.130    414
  Planarity :  0.003   0.026    444
  Dihedral  : 10.713  54.476    363
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.03 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -2.96 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 329 
 TYR   0.010   0.001   TYR F 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01223 (   74)
  hydrogen bonds       : angle       3.86680 (  222)
  SS BOND              : bond        0.00408 (    6)
  SS BOND              : angle       1.44702 (   12)
  covalent geometry    : bond        0.00254 ( 2664)
  covalent geometry    : angle       0.61106 ( 3558)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 10
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7568 (t0)
REVERT: C  314 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.6894 (t0)
REVERT: F  314 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6917 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 12
  average time/residue: 0.2981
  time to fit residues: 4.9290
Evaluate side-chains
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain C residue  314 ASP
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain E residue  291 CYS
Chi-restraints excluded: chain F residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 296 ASN ** 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 = 0.4609 r_free = 0.4609 target = 0.154728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.137668 restraints weight = 9789.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 2.60
r_work: 0.4366 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4247 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.5309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2670  Z= 0.145
  Angle     :  0.644   5.069   3570  Z= 0.346
  Chirality :  0.054   0.134    414
  Planarity :  0.003   0.023    444
  Dihedral  : 10.878  55.156    363
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.71 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -3.00 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 329 
 TYR   0.010   0.002   TYR F 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01367 (   74)
  hydrogen bonds       : angle       3.93161 (  222)
  SS BOND              : bond        0.00356 (    6)
  SS BOND              : angle       1.45700 (   12)
  covalent geometry    : bond        0.00327 ( 2664)
  covalent geometry    : angle       0.63925 ( 3558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3896.14 seconds
wall clock time: 67 minutes 40.72 seconds (4060.72 seconds total)