Starting phenix.real_space_refine
on Fri Aug 22 15:54:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r3t_18874/08_2025/8r3t_18874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r3t_18874/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r3t_18874/08_2025/8r3t_18874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r3t_18874/08_2025/8r3t_18874.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r3t_18874/08_2025/8r3t_18874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r3t_18874/08_2025/8r3t_18874.map"
  }
  resolution = 3.1
  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=   0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.38, per 1000 atoms: 0.25
  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: 0.77
  Conformation dependent library (CDL) restraints added in 147.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.16
  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: 1.10

  Time building geometry restraints manager: 1.02 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: 0.00
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:             5.160
  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:             0.040
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.040
  Find NCS groups from input model:        0.070
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.820
-------------------------------------------------------------------------------
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 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: -1.86 (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
 TYR   0.097   0.038   TYR B 310 
 HIS   0.009   0.003   HIS A 329 

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

*********************** 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  : 0.163 
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: 0.1049
  time to fit residues: 3.7142
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  : 0.154 
-------------------------------------------------------------------------------
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 27 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4744 r_free = 0.4744 target = 0.162810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.142679 restraints weight = 8949.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 2.66
r_work: 0.4477 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.4347 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.4347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2670  Z= 0.158
  Angle     :  0.825   7.184   3570  Z= 0.444
  Chirality :  0.055   0.132    414
  Planarity :  0.003   0.022    444
  Dihedral  : 13.049  57.495    369
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  2.34 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  :  9.29 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.70 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR A 310 
 HIS   0.006   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2664)
  covalent geometry    : angle       0.82396 ( 3558)
  SS BOND              : bond        0.00497 (    6)
  SS BOND              : angle       1.00992 (   12)
  hydrogen bonds       : bond        0.02864 (   74)
  hydrogen bonds       : angle       5.40209 (  222)

*********************** 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
  29 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 12
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7506 (t0)
REVERT: B  314 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.6873 (t0)
REVERT: C  314 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6720 (t0)
REVERT: D  314 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7287 (t70)
REVERT: F  314 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.6690 (t0)
REVERT: F  322 CYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6618 (m)
  outliers start: 17
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0694
  time to fit residues: 2.6436
Evaluate side-chains
  18 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 8
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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 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 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.166890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.148422 restraints weight = 8696.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.4537 rms_B_bonded: 2.46
r_work: 0.4426 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4302 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3518

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= 0.145
  Angle     :  0.745   6.034   3570  Z= 0.401
  Chirality :  0.055   0.133    414
  Planarity :  0.003   0.027    444
  Dihedral  : 12.503  58.585    368
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  :  8.33 %
    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 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: -2.75 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A 310 
 HIS   0.004   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2664)
  covalent geometry    : angle       0.73931 ( 3558)
  SS BOND              : bond        0.00299 (    6)
  SS BOND              : angle       1.78613 (   12)
  hydrogen bonds       : bond        0.02088 (   74)
  hydrogen bonds       : angle       4.53830 (  222)

*********************** 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
  25 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 10
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7576 (t0)
REVERT: B  314 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7030 (t0)
REVERT: C  314 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.6748 (t0)
REVERT: D  314 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7241 (t0)
REVERT: F  314 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.6870 (t0)
REVERT: F  322 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6916 (m)
  outliers start: 15
  outliers final: 3
  residues processed: 20
  average time/residue: 0.0509
  time to fit residues: 1.8025
Evaluate side-chains
  20 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 11
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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  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 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0170
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6018

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.167137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.148911 restraints weight = 8724.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4554 rms_B_bonded: 2.46
r_work: 0.4445 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.4323 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.3875

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     :  0.689   5.666   3570  Z= 0.371
  Chirality :  0.054   0.130    414
  Planarity :  0.003   0.026    444
  Dihedral  : 11.891  59.596    365
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  :  9.62 %
    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 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: -2.75 (0.35), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.27), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2664)
  covalent geometry    : angle       0.68383 ( 3558)
  SS BOND              : bond        0.00681 (    6)
  SS BOND              : angle       1.64501 (   12)
  hydrogen bonds       : bond        0.01621 (   74)
  hydrogen bonds       : angle       4.17547 (  222)

*********************** 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
  22 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 11
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7579 (t0)
REVERT: B  314 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.6977 (t0)
REVERT: C  314 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.6728 (t0)
REVERT: D  314 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7118 (t0)
REVERT: F  314 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.6797 (t0)
REVERT: F  322 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6953 (m)
  outliers start: 11
  outliers final: 1
  residues processed: 16
  average time/residue: 0.0825
  time to fit residues: 1.9687
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  : 0.161 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
D 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 = 0.4580 r_free = 0.4580 target = 0.160602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.142780 restraints weight = 9093.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.4480 rms_B_bonded: 2.50
r_work: 0.4392 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.4279 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2670  Z= 0.162
  Angle     :  0.691   5.713   3570  Z= 0.373
  Chirality :  0.054   0.132    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.608  57.688    365
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 11.54 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.76 (0.35), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.27), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2664)
  covalent geometry    : angle       0.68676 ( 3558)
  SS BOND              : bond        0.00620 (    6)
  SS BOND              : angle       1.53069 (   12)
  hydrogen bonds       : bond        0.01516 (   74)
  hydrogen bonds       : angle       4.31237 (  222)

*********************** 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
  24 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 10
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7514 (t0)
REVERT: B  314 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.6977 (t0)
REVERT: C  314 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6799 (t0)
REVERT: F  314 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.6695 (t0)
REVERT: F  322 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6950 (m)
  outliers start: 14
  outliers final: 3
  residues processed: 19
  average time/residue: 0.0791
  time to fit residues: 2.2470
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  : 0.194 
-------------------------------------------------------------------------------
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  296 ASN
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 22 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN
D 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 = 0.4629 r_free = 0.4629 target = 0.156990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.139428 restraints weight = 9471.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.4483 rms_B_bonded: 2.59
r_work: 0.4384 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4271 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.4615

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= 0.143
  Angle     :  0.664   5.606   3570  Z= 0.357
  Chirality :  0.054   0.130    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.501  57.365    365
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 13.14 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.84 (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
 TYR   0.007   0.001   TYR F 310 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2664)
  covalent geometry    : angle       0.65931 ( 3558)
  SS BOND              : bond        0.00491 (    6)
  SS BOND              : angle       1.46500 (   12)
  hydrogen bonds       : bond        0.01479 (   74)
  hydrogen bonds       : angle       4.28474 (  222)

*********************** 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
  22 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 10
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7511 (t0)
REVERT: B  314 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.6914 (t0)
REVERT: C  314 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6762 (t0)
REVERT: F  314 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6729 (t0)
  outliers start: 12
  outliers final: 3
  residues processed: 17
  average time/residue: 0.0804
  time to fit residues: 2.0301
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  : 0.143 
-------------------------------------------------------------------------------
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  296 ASN
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 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.155596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.138142 restraints weight = 9653.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 2.55
r_work: 0.4364 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.4250 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2670  Z= 0.163
  Angle     :  0.676   5.439   3570  Z= 0.365
  Chirality :  0.055   0.132    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.515  57.314    365
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 13.78 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 41.67 %
    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: -2.90 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.26), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 2664)
  covalent geometry    : angle       0.67027 ( 3558)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       1.67527 (   12)
  hydrogen bonds       : bond        0.01486 (   74)
  hydrogen bonds       : angle       4.27421 (  222)

*********************** 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
  21 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 10
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7511 (t0)
REVERT: B  314 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.6976 (t0)
REVERT: C  314 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6785 (t0)
REVERT: F  314 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.6795 (t0)
  outliers start: 11
  outliers final: 3
  residues processed: 16
  average time/residue: 0.0869
  time to fit residues: 2.0384
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  : 0.160 
-------------------------------------------------------------------------------
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 D residue  296 ASN
Chi-restraints excluded: chain E residue  291 CYS
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 19 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
D 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.153894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.134178 restraints weight = 9483.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4498 rms_B_bonded: 2.62
r_work: 0.4389 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.4279 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4869

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= 0.120
  Angle     :  0.647   5.367   3570  Z= 0.348
  Chirality :  0.054   0.130    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.113  56.963    363
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.03 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 50.00 %
    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: -2.91 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR F 310 
 HIS   0.002   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2664)
  covalent geometry    : angle       0.64103 ( 3558)
  SS BOND              : bond        0.00539 (    6)
  SS BOND              : angle       1.62213 (   12)
  hydrogen bonds       : bond        0.01384 (   74)
  hydrogen bonds       : angle       4.17021 (  222)

*********************** 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
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7561 (t0)
REVERT: B  314 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.6928 (t0)
REVERT: C  314 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.6751 (t0)
REVERT: F  314 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.6761 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 12
  average time/residue: 0.0890
  time to fit residues: 1.5575
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  : 0.154 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.154762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.137464 restraints weight = 9666.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.4457 rms_B_bonded: 2.57
r_work: 0.4361 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4246 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.5072

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= 0.142
  Angle     :  0.655   5.431   3570  Z= 0.352
  Chirality :  0.054   0.133    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.010  56.386    363
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.35 %
    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 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: -2.93 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.26), residues: 342

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2664)
  covalent geometry    : angle       0.64951 ( 3558)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       1.54792 (   12)
  hydrogen bonds       : bond        0.01431 (   74)
  hydrogen bonds       : angle       4.15818 (  222)

*********************** 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: 7
    poor density    : 9
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7489 (t0)
REVERT: B  314 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.6964 (t0)
REVERT: C  314 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.6802 (t0)
REVERT: E  331 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6683 (mptt)
REVERT: F  314 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.6773 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 12
  average time/residue: 0.0911
  time to fit residues: 1.5828
Evaluate side-chains
  15 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.158296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.141252 restraints weight = 9270.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 2.37
r_work: 0.4380 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.4273 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.4273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.141   2670  Z= 0.266
  Angle     :  1.394  59.197   3570  Z= 0.850
  Chirality :  0.055   0.232    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.013  56.383    363
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  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 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: -2.95 (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
 TYR   0.009   0.002   TYR A 310 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 2664)
  covalent geometry    : angle       1.39304 ( 3558)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.62831 (   12)
  hydrogen bonds       : bond        0.01724 (   74)
  hydrogen bonds       : angle       4.16312 (  222)

********************** 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
  16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7536 (t0)
REVERT: B  314 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7017 (t0)
REVERT: C  314 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6868 (t0)
REVERT: D  314 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7402 (t0)
REVERT: E  331 LYS cc_start: 0.6955 (mtpt) cc_final: 0.6727 (mptt)
REVERT: F  314 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.6838 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 11
  average time/residue: 0.0948
  time to fit residues: 1.5108
Evaluate side-chains
  15 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 9
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 2 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:
C 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.158172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.141170 restraints weight = 9294.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 2.37
r_work: 0.4383 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4276 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.141   2670  Z= 0.266
  Angle     :  1.394  59.197   3570  Z= 0.850
  Chirality :  0.055   0.232    414
  Planarity :  0.003   0.025    444
  Dihedral  : 11.013  56.383    363
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  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 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: -2.95 (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
 TYR   0.009   0.002   TYR A 310 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 2664)
  covalent geometry    : angle       1.39304 ( 3558)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.62831 (   12)
  hydrogen bonds       : bond        0.01724 (   74)
  hydrogen bonds       : angle       4.16312 (  222)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2173.25 seconds
wall clock time: 37 minutes 34.64 seconds (2254.64 seconds total)