Starting phenix.real_space_refine
on Sat Aug 23 14:59:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9e_39075/08_2025/8y9e_39075.map"
  }
  resolution = 2.95
  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=   0.002 sd=   0.094
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      80      5.16       5
     C    8412      2.51       5
     N    2156      2.21       5
     O    2428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  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: 13076
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3269
          Classifications: {'peptide': 410}
          Link IDs: {'PTRANS': 27, 'TRANS': 382}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.44, per 1000 atoms: 0.19
  Number of scatterers: 13076
  At special positions: 0
  Unit cell: (98.58, 111.3, 102.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      80     16.00
     O    2428      8.00
     N    2156      7.00
     C    8412      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.74
  Conformation dependent library (CDL) restraints added in 425.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3088

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 4 sheets defined
      50.7% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 34
    Processing helix  chain 'A' and resid 38 through 60
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 62 through 76
    Processing helix  chain 'A' and resid 77 through 81
    Processing helix  chain 'A' and resid 137 through 151
      removed outlier: 4.354A  pdb=" N   LYS A 141 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 168
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 220 through 237
      removed outlier: 3.917A  pdb=" N   ASP A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
    Processing helix  chain 'A' and resid 251 through 257
      removed outlier: 4.076A  pdb=" N   HIS A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 297
    Processing helix  chain 'A' and resid 303 through 321
      removed outlier: 3.746A  pdb=" N   ILE A 312 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 329
      removed outlier: 3.631A  pdb=" N   LYS A 329 " --> pdb=" O   PRO A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 377
    Processing helix  chain 'A' and resid 378 through 393
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 4.089A  pdb=" N   SER A 429 " --> pdb=" O   PRO A 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 34
    Processing helix  chain 'B' and resid 38 through 60
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 62 through 76
    Processing helix  chain 'B' and resid 77 through 81
    Processing helix  chain 'B' and resid 137 through 151
      removed outlier: 4.354A  pdb=" N   LYS B 141 " --> pdb=" O   GLU B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 168
      Proline residue:  B 165  - end of helix
    Processing helix  chain 'B' and resid 170 through 177
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 220 through 237
      removed outlier: 3.918A  pdb=" N   ASP B 227 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 250
    Processing helix  chain 'B' and resid 251 through 257
      removed outlier: 4.076A  pdb=" N   HIS B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR B 257 " --> pdb=" O   LYS B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 297
    Processing helix  chain 'B' and resid 303 through 321
      removed outlier: 3.745A  pdb=" N   ILE B 312 " --> pdb=" O   TYR B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 329
      removed outlier: 3.630A  pdb=" N   LYS B 329 " --> pdb=" O   PRO B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 377
    Processing helix  chain 'B' and resid 378 through 393
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 426 through 430
      removed outlier: 4.089A  pdb=" N   SER B 429 " --> pdb=" O   PRO B 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 34
    Processing helix  chain 'C' and resid 38 through 60
      Proline residue:  C  50  - end of helix
    Processing helix  chain 'C' and resid 62 through 76
    Processing helix  chain 'C' and resid 77 through 81
    Processing helix  chain 'C' and resid 137 through 151
      removed outlier: 4.354A  pdb=" N   LYS C 141 " --> pdb=" O   GLU C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 168
      Proline residue:  C 165  - end of helix
    Processing helix  chain 'C' and resid 170 through 177
    Processing helix  chain 'C' and resid 210 through 218
    Processing helix  chain 'C' and resid 220 through 237
      removed outlier: 3.917A  pdb=" N   ASP C 227 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 250
    Processing helix  chain 'C' and resid 251 through 257
      removed outlier: 4.076A  pdb=" N   HIS C 255 " --> pdb=" O   GLU C 251 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR C 257 " --> pdb=" O   LYS C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 297
    Processing helix  chain 'C' and resid 303 through 321
      removed outlier: 3.746A  pdb=" N   ILE C 312 " --> pdb=" O   TYR C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 329
      removed outlier: 3.631A  pdb=" N   LYS C 329 " --> pdb=" O   PRO C 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 377
    Processing helix  chain 'C' and resid 378 through 393
    Processing helix  chain 'C' and resid 394 through 399
    Processing helix  chain 'C' and resid 426 through 430
      removed outlier: 4.089A  pdb=" N   SER C 429 " --> pdb=" O   PRO C 426 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 34
    Processing helix  chain 'D' and resid 38 through 60
      Proline residue:  D  50  - end of helix
    Processing helix  chain 'D' and resid 62 through 76
    Processing helix  chain 'D' and resid 77 through 81
    Processing helix  chain 'D' and resid 137 through 151
      removed outlier: 4.353A  pdb=" N   LYS D 141 " --> pdb=" O   GLU D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 168
      Proline residue:  D 165  - end of helix
    Processing helix  chain 'D' and resid 170 through 177
    Processing helix  chain 'D' and resid 210 through 218
    Processing helix  chain 'D' and resid 220 through 237
      removed outlier: 3.918A  pdb=" N   ASP D 227 " --> pdb=" O   ASP D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 250
    Processing helix  chain 'D' and resid 251 through 257
      removed outlier: 4.075A  pdb=" N   HIS D 255 " --> pdb=" O   GLU D 251 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR D 257 " --> pdb=" O   LYS D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 297
    Processing helix  chain 'D' and resid 303 through 321
      removed outlier: 3.745A  pdb=" N   ILE D 312 " --> pdb=" O   TYR D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 325 through 329
      removed outlier: 3.631A  pdb=" N   LYS D 329 " --> pdb=" O   PRO D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 377
    Processing helix  chain 'D' and resid 378 through 393
    Processing helix  chain 'D' and resid 394 through 399
    Processing helix  chain 'D' and resid 426 through 430
      removed outlier: 4.089A  pdb=" N   SER D 429 " --> pdb=" O   PRO D 426 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203
      removed outlier: 3.738A  pdb=" N   THR A 203 " --> pdb=" O   ASP A 195 " (cutoff:3.500A)
      removed outlier: 10.545A  pdb=" N   VAL A 260 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
      removed outlier: 11.456A  pdb=" N   LYS A 284 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ARG A 262 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLU A 282 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   HIS A 335 " --> pdb=" O   THR A 356 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   TYR A 413 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU A 104 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 117 " --> pdb=" O   MET A 196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 203
      removed outlier: 3.739A  pdb=" N   THR B 203 " --> pdb=" O   ASP B 195 " (cutoff:3.500A)
      removed outlier: 10.545A  pdb=" N   VAL B 260 " --> pdb=" O   LYS B 284 " (cutoff:3.500A)
      removed outlier: 11.455A  pdb=" N   LYS B 284 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG B 262 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLU B 282 " --> pdb=" O   ARG B 262 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   HIS B 335 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR B 413 " --> pdb=" O   PRO B 351 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU B 104 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE B 117 " --> pdb=" O   MET B 196 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203
      removed outlier: 3.739A  pdb=" N   THR C 203 " --> pdb=" O   ASP C 195 " (cutoff:3.500A)
      removed outlier: 10.544A  pdb=" N   VAL C 260 " --> pdb=" O   LYS C 284 " (cutoff:3.500A)
      removed outlier: 11.455A  pdb=" N   LYS C 284 " --> pdb=" O   VAL C 260 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ARG C 262 " --> pdb=" O   GLU C 282 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLU C 282 " --> pdb=" O   ARG C 262 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   HIS C 335 " --> pdb=" O   THR C 356 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   TYR C 413 " --> pdb=" O   PRO C 351 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLU C 104 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE C 117 " --> pdb=" O   MET C 196 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 202 through 203
      removed outlier: 3.738A  pdb=" N   THR D 203 " --> pdb=" O   ASP D 195 " (cutoff:3.500A)
      removed outlier: 10.544A  pdb=" N   VAL D 260 " --> pdb=" O   LYS D 284 " (cutoff:3.500A)
      removed outlier: 11.455A  pdb=" N   LYS D 284 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ARG D 262 " --> pdb=" O   GLU D 282 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   GLU D 282 " --> pdb=" O   ARG D 262 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   HIS D 335 " --> pdb=" O   THR D 356 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   TYR D 413 " --> pdb=" O   PRO D 351 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU D 104 " --> pdb=" O   THR D 120 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE D 117 " --> pdb=" O   MET D 196 " (cutoff:3.500A)

    728 hydrogen bonds defined for protein.
    2076 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: 1.67

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4128
        1.34 -     1.45: 2490
        1.45 -     1.57: 6714
        1.57 -     1.69: 0
        1.69 -     1.80: 140
  Bond restraints: 13472
  Sorted by residual:
  bond pdb=" CB  MET B  81 "
       pdb=" CG  MET B  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.461  0.059 3.00e-02 1.11e+03 3.81e+00
  bond pdb=" CB  MET D  81 "
       pdb=" CG  MET D  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.058 3.00e-02 1.11e+03 3.80e+00
  bond pdb=" CB  MET A  81 "
       pdb=" CG  MET A  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.058 3.00e-02 1.11e+03 3.79e+00
  bond pdb=" CB  MET C  81 "
       pdb=" CG  MET C  81 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.058 3.00e-02 1.11e+03 3.79e+00
  bond pdb=" CG  LEU B 143 "
       pdb=" CD1 LEU B 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.44e+00
  ... (remaining 13467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 17670
        1.51 -     3.02: 558
        3.02 -     4.52: 84
        4.52 -     6.03: 12
        6.03 -     7.54: 4
  Bond angle restraints: 18328
  Sorted by residual:
  angle pdb=" CA  GLU A 359 "
        pdb=" CB  GLU A 359 "
        pdb=" CG  GLU A 359 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CA  GLU D 359 "
        pdb=" CB  GLU D 359 "
        pdb=" CG  GLU D 359 "
      ideal   model   delta    sigma   weight residual
     114.10  121.63   -7.53 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CA  GLU B 359 "
        pdb=" CB  GLU B 359 "
        pdb=" CG  GLU B 359 "
      ideal   model   delta    sigma   weight residual
     114.10  121.62   -7.52 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CA  GLU C 359 "
        pdb=" CB  GLU C 359 "
        pdb=" CG  GLU C 359 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" N   ASN C  86 "
        pdb=" CA  ASN C  86 "
        pdb=" C   ASN C  86 "
      ideal   model   delta    sigma   weight residual
     110.19  107.20    2.99 1.24e+00 6.50e-01 5.82e+00
  ... (remaining 18323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 7308
       17.02 -    34.05: 548
       34.05 -    51.07: 104
       51.07 -    68.09: 8
       68.09 -    85.12: 8
  Dihedral angle restraints: 7976
    sinusoidal: 3164
      harmonic: 4812
  Sorted by residual:
  dihedral pdb=" CA  PRO B  85 "
           pdb=" C   PRO B  85 "
           pdb=" N   ASN B  86 "
           pdb=" CA  ASN B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.07   16.93     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  PRO A  85 "
           pdb=" C   PRO A  85 "
           pdb=" N   ASN A  86 "
           pdb=" CA  ASN A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.07   16.93     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  PRO C  85 "
           pdb=" C   PRO C  85 "
           pdb=" N   ASN C  86 "
           pdb=" CA  ASN C  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 7973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1016
       0.032 -    0.063: 603
       0.063 -    0.095: 225
       0.095 -    0.127: 92
       0.127 -    0.158: 12
  Chirality restraints: 1948
  Sorted by residual:
  chirality pdb=" CA  PRO A  26 "
            pdb=" N   PRO A  26 "
            pdb=" C   PRO A  26 "
            pdb=" CB  PRO A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  PRO D  26 "
            pdb=" N   PRO D  26 "
            pdb=" C   PRO D  26 "
            pdb=" CB  PRO D  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CA  PRO C  26 "
            pdb=" N   PRO C  26 "
            pdb=" C   PRO C  26 "
            pdb=" CB  PRO C  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.80e-01
  ... (remaining 1945 not shown)

  Planarity restraints: 2344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 171 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO C 172 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C 172 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 172 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 171 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B 172 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 172 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 172 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 171 "    0.030 5.00e-02 4.00e+02   4.50e-02 3.23e+00
        pdb=" N   PRO D 172 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO D 172 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 172 "    0.025 5.00e-02 4.00e+02
  ... (remaining 2341 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 280
        2.68 -     3.24: 13313
        3.24 -     3.79: 21161
        3.79 -     4.35: 30008
        4.35 -     4.90: 49430
  Nonbonded interactions: 114192
  Sorted by model distance:
  nonbonded pdb=" N   GLU D 359 "
            pdb=" OE1 GLU D 359 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" N   GLU C 359 "
            pdb=" OE1 GLU C 359 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" N   GLU B 359 "
            pdb=" OE1 GLU B 359 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" N   GLU A 359 "
            pdb=" OE1 GLU A 359 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" NH1 ARG A 146 "
            pdb=" OE1 GLN A 149 "
     model   vdw
     2.209 3.120
  ... (remaining 114187 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.670
  Find NCS groups from input model:        0.100
  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:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
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      :  0.010   0.069  13472  Z= 0.374
  Angle     :  0.656   7.539  18328  Z= 0.354
  Chirality :  0.046   0.158   1948
  Planarity :  0.004   0.045   2344
  Dihedral  : 12.358  85.119   4888
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.28 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.86 (0.17), residues: 1632
  helix: -2.44 (0.15), residues: 692
  sheet: -2.18 (0.26), residues: 340
  loop : -2.66 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  43 
 TYR   0.014   0.002   TYR B 280 
 PHE   0.011   0.001   PHE A 310 
 TRP   0.012   0.002   TRP D  27 
 HIS   0.005   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00971 (13472)
  covalent geometry    : angle       0.65589 (18328)
  hydrogen bonds       : bond        0.16918 (  728)
  hydrogen bonds       : angle       7.78799 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 261
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A   37 GLN cc_start: 0.7773 (mt0) cc_final: 0.7534 (mt0)
REVERT: A  205 LYS cc_start: 0.7779 (tttt) cc_final: 0.7460 (tttm)
REVERT: A  259 MET cc_start: 0.7523 (mtm) cc_final: 0.7255 (mtp)
REVERT: A  268 ASP cc_start: 0.7897 (m-30) cc_final: 0.7663 (m-30)
REVERT: A  276 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6560 (mtp85)
REVERT: A  329 LYS cc_start: 0.7172 (mtpt) cc_final: 0.6181 (mptm)
REVERT: A  341 GLU cc_start: 0.7824 (pt0) cc_final: 0.7554 (pt0)
REVERT: B   37 GLN cc_start: 0.7801 (mt0) cc_final: 0.7572 (mt0)
REVERT: B  205 LYS cc_start: 0.7781 (tttt) cc_final: 0.7460 (tttm)
REVERT: B  259 MET cc_start: 0.7515 (mtm) cc_final: 0.7220 (mtp)
REVERT: B  268 ASP cc_start: 0.7943 (m-30) cc_final: 0.7666 (m-30)
REVERT: B  276 ARG cc_start: 0.6948 (mtp85) cc_final: 0.6576 (mtp85)
REVERT: B  329 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6147 (mptm)
REVERT: B  341 GLU cc_start: 0.7823 (pt0) cc_final: 0.7580 (pt0)
REVERT: C   37 GLN cc_start: 0.7778 (mt0) cc_final: 0.7539 (mt0)
REVERT: C  205 LYS cc_start: 0.7779 (tttt) cc_final: 0.7454 (tttm)
REVERT: C  259 MET cc_start: 0.7524 (mtm) cc_final: 0.7255 (mtp)
REVERT: C  268 ASP cc_start: 0.7882 (m-30) cc_final: 0.7640 (m-30)
REVERT: C  276 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6570 (mtp85)
REVERT: C  329 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6184 (mptm)
REVERT: C  341 GLU cc_start: 0.7818 (pt0) cc_final: 0.7558 (pt0)
REVERT: D   37 GLN cc_start: 0.7780 (mt0) cc_final: 0.7534 (mt0)
REVERT: D  205 LYS cc_start: 0.7780 (tttt) cc_final: 0.7459 (tttm)
REVERT: D  259 MET cc_start: 0.7521 (mtm) cc_final: 0.7251 (mtp)
REVERT: D  268 ASP cc_start: 0.7892 (m-30) cc_final: 0.7652 (m-30)
REVERT: D  276 ARG cc_start: 0.6972 (mtp85) cc_final: 0.6565 (mtp85)
REVERT: D  329 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6193 (mptm)
REVERT: D  341 GLU cc_start: 0.7821 (pt0) cc_final: 0.7545 (pt0)
  outliers start: 8
  outliers final: 4
  residues processed: 261
  average time/residue: 0.6265
  time to fit residues: 177.8694
Evaluate side-chains
  197 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 193
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain D residue  170 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    8.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 255 HIS
A 385 HIS
B 110 GLN
B 255 HIS
B 385 HIS
C 110 GLN
C 255 HIS
C 385 HIS
D 110 GLN
D 255 HIS
D 385 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.158666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.121979 restraints weight = 14175.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.88
r_work: 0.3257 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13472  Z= 0.153
  Angle     :  0.564   5.013  18328  Z= 0.297
  Chirality :  0.044   0.159   1948
  Planarity :  0.005   0.044   2344
  Dihedral  :  4.563  15.177   1788
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  8.59 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.20), residues: 1632
  helix: -0.62 (0.18), residues: 712
  sheet: -1.57 (0.28), residues: 340
  loop : -0.97 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 146 
 TYR   0.024   0.002   TYR B 264 
 PHE   0.012   0.001   PHE B 248 
 TRP   0.010   0.002   TRP A  27 
 HIS   0.004   0.001   HIS D  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13472)
  covalent geometry    : angle       0.56401 (18328)
  hydrogen bonds       : bond        0.03949 (  728)
  hydrogen bonds       : angle       6.11843 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 234
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7478 (mm-30)
REVERT: A  173 GLU cc_start: 0.7746 (tt0) cc_final: 0.7538 (tt0)
REVERT: A  205 LYS cc_start: 0.8185 (tttt) cc_final: 0.7809 (tttp)
REVERT: A  259 MET cc_start: 0.7765 (mtm) cc_final: 0.7551 (mtm)
REVERT: A  311 LYS cc_start: 0.7422 (mmpt) cc_final: 0.6803 (mmpt)
REVERT: A  329 LYS cc_start: 0.6640 (mtpt) cc_final: 0.5398 (mptm)
REVERT: A  423 TYR cc_start: 0.8430 (m-80) cc_final: 0.8194 (m-80)
REVERT: B  113 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7501 (mm-30)
REVERT: B  205 LYS cc_start: 0.8196 (tttt) cc_final: 0.7831 (tttp)
REVERT: B  259 MET cc_start: 0.7751 (mtm) cc_final: 0.7430 (mtp)
REVERT: B  311 LYS cc_start: 0.7434 (mmpt) cc_final: 0.6818 (mmpt)
REVERT: B  329 LYS cc_start: 0.6659 (mtpt) cc_final: 0.5394 (mptm)
REVERT: B  341 GLU cc_start: 0.8108 (pt0) cc_final: 0.7902 (pt0)
REVERT: B  423 TYR cc_start: 0.8430 (m-80) cc_final: 0.8197 (m-80)
REVERT: C  113 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7478 (mm-30)
REVERT: C  173 GLU cc_start: 0.7761 (tt0) cc_final: 0.7556 (tt0)
REVERT: C  205 LYS cc_start: 0.8190 (tttt) cc_final: 0.7814 (tttp)
REVERT: C  234 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6930 (mtpp)
REVERT: C  259 MET cc_start: 0.7757 (mtm) cc_final: 0.7543 (mtm)
REVERT: C  311 LYS cc_start: 0.7434 (mmpt) cc_final: 0.6814 (mmpt)
REVERT: C  329 LYS cc_start: 0.6637 (mtpt) cc_final: 0.5390 (mptm)
REVERT: C  423 TYR cc_start: 0.8426 (m-80) cc_final: 0.8193 (m-80)
REVERT: D  113 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7487 (mm-30)
REVERT: D  173 GLU cc_start: 0.7751 (tt0) cc_final: 0.7539 (tt0)
REVERT: D  205 LYS cc_start: 0.8163 (tttt) cc_final: 0.7791 (tttp)
REVERT: D  259 MET cc_start: 0.7751 (mtm) cc_final: 0.7538 (mtm)
REVERT: D  311 LYS cc_start: 0.7411 (mmpt) cc_final: 0.6791 (mmpt)
REVERT: D  329 LYS cc_start: 0.6636 (mtpt) cc_final: 0.5403 (mptm)
REVERT: D  423 TYR cc_start: 0.8423 (m-80) cc_final: 0.8192 (m-80)
  outliers start: 37
  outliers final: 16
  residues processed: 251
  average time/residue: 0.5970
  time to fit residues: 163.1759
Evaluate side-chains
  208 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  342 MET
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  342 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 145 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 144 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 114 optimal weight:    0.5980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 334 ASN
B 255 HIS
C 255 HIS
C 334 ASN
D 255 HIS
D 334 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.158500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121923 restraints weight = 14256.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.90
r_work: 0.3242 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13472  Z= 0.150
  Angle     :  0.552   4.929  18328  Z= 0.291
  Chirality :  0.044   0.141   1948
  Planarity :  0.004   0.041   2344
  Dihedral  :  4.396  16.079   1780
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.55 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.21), residues: 1632
  helix: -0.05 (0.18), residues: 720
  sheet: -1.48 (0.28), residues: 348
  loop : -0.67 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 331 
 TYR   0.022   0.002   TYR A 264 
 PHE   0.010   0.001   PHE B 310 
 TRP   0.011   0.001   TRP D 317 
 HIS   0.004   0.001   HIS C  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13472)
  covalent geometry    : angle       0.55217 (18328)
  hydrogen bonds       : bond        0.03593 (  728)
  hydrogen bonds       : angle       5.85617 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7780 (tt0) cc_final: 0.7442 (mm-30)
REVERT: A  173 GLU cc_start: 0.7728 (tt0) cc_final: 0.7397 (tt0)
REVERT: A  205 LYS cc_start: 0.8219 (tttt) cc_final: 0.7838 (tttp)
REVERT: A  230 GLU cc_start: 0.6958 (tt0) cc_final: 0.6565 (tm-30)
REVERT: A  234 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6487 (mmpt)
REVERT: A  259 MET cc_start: 0.7774 (mtm) cc_final: 0.7417 (mtp)
REVERT: A  274 LYS cc_start: 0.8075 (mttt) cc_final: 0.7762 (mttp)
REVERT: A  311 LYS cc_start: 0.7367 (mmpt) cc_final: 0.6690 (mmtt)
REVERT: A  329 LYS cc_start: 0.6579 (mtpt) cc_final: 0.5289 (mptm)
REVERT: A  359 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7340 (pm20)
REVERT: B  113 GLU cc_start: 0.7771 (tt0) cc_final: 0.7448 (mm-30)
REVERT: B  205 LYS cc_start: 0.8204 (tttt) cc_final: 0.7817 (tttp)
REVERT: B  230 GLU cc_start: 0.6944 (tt0) cc_final: 0.6527 (tm-30)
REVERT: B  234 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6804 (mmpt)
REVERT: B  259 MET cc_start: 0.7774 (mtm) cc_final: 0.7393 (mtp)
REVERT: B  274 LYS cc_start: 0.7992 (mttt) cc_final: 0.7704 (mttp)
REVERT: B  311 LYS cc_start: 0.7353 (mmpt) cc_final: 0.6679 (mmtt)
REVERT: B  329 LYS cc_start: 0.6683 (mtpt) cc_final: 0.5399 (mptm)
REVERT: B  359 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7363 (pm20)
REVERT: C  113 GLU cc_start: 0.7767 (tt0) cc_final: 0.7429 (mm-30)
REVERT: C  173 GLU cc_start: 0.7752 (tt0) cc_final: 0.7420 (tt0)
REVERT: C  205 LYS cc_start: 0.8211 (tttt) cc_final: 0.7828 (tttp)
REVERT: C  227 ASP cc_start: 0.6841 (m-30) cc_final: 0.6635 (m-30)
REVERT: C  230 GLU cc_start: 0.6972 (tt0) cc_final: 0.6416 (tm-30)
REVERT: C  234 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6489 (mmpt)
REVERT: C  259 MET cc_start: 0.7782 (mtm) cc_final: 0.7427 (mtp)
REVERT: C  274 LYS cc_start: 0.8048 (mttt) cc_final: 0.7689 (mttp)
REVERT: C  311 LYS cc_start: 0.7355 (mmpt) cc_final: 0.6683 (mmtt)
REVERT: C  329 LYS cc_start: 0.6589 (mtpt) cc_final: 0.5304 (mptm)
REVERT: C  359 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7363 (pm20)
REVERT: D  113 GLU cc_start: 0.7808 (tt0) cc_final: 0.7419 (mm-30)
REVERT: D  173 GLU cc_start: 0.7722 (tt0) cc_final: 0.7389 (tt0)
REVERT: D  205 LYS cc_start: 0.8209 (tttt) cc_final: 0.7829 (tttp)
REVERT: D  230 GLU cc_start: 0.6967 (tt0) cc_final: 0.6589 (tm-30)
REVERT: D  234 LYS cc_start: 0.6945 (mmtt) cc_final: 0.6489 (mmpt)
REVERT: D  259 MET cc_start: 0.7773 (mtm) cc_final: 0.7414 (mtp)
REVERT: D  274 LYS cc_start: 0.8075 (mttt) cc_final: 0.7759 (mttp)
REVERT: D  311 LYS cc_start: 0.7336 (mmpt) cc_final: 0.6658 (mmtt)
REVERT: D  329 LYS cc_start: 0.6574 (mtpt) cc_final: 0.5288 (mptm)
REVERT: D  359 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7385 (pm20)
  outliers start: 44
  outliers final: 25
  residues processed: 246
  average time/residue: 0.6718
  time to fit residues: 179.2383
Evaluate side-chains
  218 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  318 ASP
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  342 MET
Chi-restraints excluded: chain B residue  359 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  342 MET
Chi-restraints excluded: chain D residue  359 GLU
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 156 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 144 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 124 optimal weight:    0.1980
   chunk 42 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
B 255 HIS
B 334 ASN
C 255 HIS
D 255 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.159549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.122866 restraints weight = 14278.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.90
r_work: 0.3259 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13472  Z= 0.130
  Angle     :  0.531   4.840  18328  Z= 0.279
  Chirality :  0.043   0.141   1948
  Planarity :  0.005   0.042   2344
  Dihedral  :  4.292  16.499   1780
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 12.39 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.21), residues: 1632
  helix:  0.17 (0.19), residues: 720
  sheet: -1.51 (0.28), residues: 348
  loop : -0.48 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 331 
 TYR   0.021   0.001   TYR D 264 
 PHE   0.009   0.001   PHE A 226 
 TRP   0.010   0.001   TRP A  27 
 HIS   0.004   0.001   HIS D  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13472)
  covalent geometry    : angle       0.53060 (18328)
  hydrogen bonds       : bond        0.03356 (  728)
  hydrogen bonds       : angle       5.75245 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 199
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7590 (tt0) cc_final: 0.7212 (mm-30)
REVERT: A  121 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8261 (pt)
REVERT: A  205 LYS cc_start: 0.8194 (tttt) cc_final: 0.7826 (tttp)
REVERT: A  230 GLU cc_start: 0.6945 (tt0) cc_final: 0.6523 (tm-30)
REVERT: A  234 LYS cc_start: 0.6691 (mmtt) cc_final: 0.6140 (mmpt)
REVERT: A  248 PHE cc_start: 0.7733 (t80) cc_final: 0.7131 (t80)
REVERT: A  259 MET cc_start: 0.7774 (mtm) cc_final: 0.7422 (mtp)
REVERT: A  274 LYS cc_start: 0.8044 (mttt) cc_final: 0.7720 (mttp)
REVERT: A  311 LYS cc_start: 0.7254 (mmpt) cc_final: 0.6591 (mmtt)
REVERT: A  329 LYS cc_start: 0.6596 (mtpt) cc_final: 0.5331 (mptm)
REVERT: A  359 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7339 (pm20)
REVERT: A  423 TYR cc_start: 0.8433 (m-80) cc_final: 0.8064 (m-80)
REVERT: B  113 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7442 (mm-30)
REVERT: B  205 LYS cc_start: 0.8186 (tttt) cc_final: 0.7794 (tttp)
REVERT: B  230 GLU cc_start: 0.6878 (tt0) cc_final: 0.6465 (tm-30)
REVERT: B  234 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6331 (mmpt)
REVERT: B  259 MET cc_start: 0.7771 (mtm) cc_final: 0.7394 (mtp)
REVERT: B  274 LYS cc_start: 0.7982 (mttt) cc_final: 0.7670 (mttp)
REVERT: B  311 LYS cc_start: 0.7241 (mmpt) cc_final: 0.6578 (mmtt)
REVERT: B  329 LYS cc_start: 0.6576 (mtpt) cc_final: 0.5284 (mptm)
REVERT: B  354 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7968 (m-10)
REVERT: B  423 TYR cc_start: 0.8440 (m-80) cc_final: 0.8080 (m-80)
REVERT: C  113 GLU cc_start: 0.7603 (tt0) cc_final: 0.7215 (mm-30)
REVERT: C  121 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8267 (pt)
REVERT: C  205 LYS cc_start: 0.8193 (tttt) cc_final: 0.7825 (tttp)
REVERT: C  227 ASP cc_start: 0.6831 (m-30) cc_final: 0.6629 (m-30)
REVERT: C  230 GLU cc_start: 0.6934 (tt0) cc_final: 0.6381 (tm-30)
REVERT: C  234 LYS cc_start: 0.6610 (mmtt) cc_final: 0.6040 (mmpt)
REVERT: C  259 MET cc_start: 0.7769 (mtm) cc_final: 0.7408 (mtp)
REVERT: C  274 LYS cc_start: 0.8015 (mttt) cc_final: 0.7714 (mttp)
REVERT: C  311 LYS cc_start: 0.7251 (mmpt) cc_final: 0.6592 (mmtt)
REVERT: C  329 LYS cc_start: 0.6581 (mtpt) cc_final: 0.5330 (mptm)
REVERT: C  359 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7342 (pm20)
REVERT: C  423 TYR cc_start: 0.8437 (m-80) cc_final: 0.8071 (m-80)
REVERT: D  113 GLU cc_start: 0.7748 (tt0) cc_final: 0.7359 (mm-30)
REVERT: D  121 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8276 (pt)
REVERT: D  205 LYS cc_start: 0.8193 (tttt) cc_final: 0.7823 (tttp)
REVERT: D  230 GLU cc_start: 0.6924 (tt0) cc_final: 0.6485 (tm-30)
REVERT: D  234 LYS cc_start: 0.6666 (mmtt) cc_final: 0.6114 (mmpt)
REVERT: D  259 MET cc_start: 0.7763 (mtm) cc_final: 0.7407 (mtp)
REVERT: D  274 LYS cc_start: 0.8031 (mttt) cc_final: 0.7711 (mttp)
REVERT: D  311 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6611 (mmtt)
REVERT: D  329 LYS cc_start: 0.6577 (mtpt) cc_final: 0.5321 (mptm)
REVERT: D  359 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (pm20)
REVERT: D  423 TYR cc_start: 0.8437 (m-80) cc_final: 0.8067 (m-80)
  outliers start: 50
  outliers final: 23
  residues processed: 232
  average time/residue: 0.6792
  time to fit residues: 171.1847
Evaluate side-chains
  213 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  359 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  342 MET
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  342 MET
Chi-restraints excluded: chain D residue  359 GLU
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 130 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 145 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0980
   chunk 131 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 90 optimal weight:    0.5980
   chunk 140 optimal weight:    0.8980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
B 255 HIS
C 255 HIS
D 255 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.161853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125417 restraints weight = 14290.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.93
r_work: 0.3307 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13472  Z= 0.110
  Angle     :  0.505   4.936  18328  Z= 0.266
  Chirality :  0.042   0.146   1948
  Planarity :  0.004   0.042   2344
  Dihedral  :  4.144  16.071   1780
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 11.97 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.21), residues: 1632
  helix:  0.61 (0.19), residues: 688
  sheet: -1.47 (0.28), residues: 344
  loop : -0.14 (0.28), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 331 
 TYR   0.020   0.001   TYR B 264 
 PHE   0.011   0.001   PHE B 248 
 TRP   0.009   0.001   TRP C 317 
 HIS   0.004   0.001   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13472)
  covalent geometry    : angle       0.50528 (18328)
  hydrogen bonds       : bond        0.03102 (  728)
  hydrogen bonds       : angle       5.61511 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 213
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7164 (mm-30)
REVERT: A  121 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8313 (pt)
REVERT: A  205 LYS cc_start: 0.8209 (tttt) cc_final: 0.7878 (tttp)
REVERT: A  230 GLU cc_start: 0.6990 (tt0) cc_final: 0.6556 (tm-30)
REVERT: A  234 LYS cc_start: 0.6640 (mmtt) cc_final: 0.6054 (mmpt)
REVERT: A  259 MET cc_start: 0.7811 (mtm) cc_final: 0.7484 (mtp)
REVERT: A  274 LYS cc_start: 0.7964 (mttt) cc_final: 0.7655 (mttp)
REVERT: A  311 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6619 (mmtt)
REVERT: A  329 LYS cc_start: 0.6566 (mtpt) cc_final: 0.5314 (mptm)
REVERT: A  423 TYR cc_start: 0.8403 (m-80) cc_final: 0.8073 (m-80)
REVERT: B  113 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (mm-30)
REVERT: B  121 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8281 (pt)
REVERT: B  205 LYS cc_start: 0.8204 (tttt) cc_final: 0.7859 (tttp)
REVERT: B  230 GLU cc_start: 0.6943 (tt0) cc_final: 0.6493 (tm-30)
REVERT: B  234 LYS cc_start: 0.6730 (mmtt) cc_final: 0.6135 (mmpt)
REVERT: B  259 MET cc_start: 0.7811 (mtm) cc_final: 0.7465 (mtp)
REVERT: B  274 LYS cc_start: 0.8005 (mttt) cc_final: 0.7685 (mttp)
REVERT: B  311 LYS cc_start: 0.7272 (mmpt) cc_final: 0.6577 (mmtt)
REVERT: B  329 LYS cc_start: 0.6685 (mtpt) cc_final: 0.5327 (mptm)
REVERT: B  423 TYR cc_start: 0.8422 (m-80) cc_final: 0.8081 (m-80)
REVERT: C  113 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7172 (mm-30)
REVERT: C  121 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8317 (pt)
REVERT: C  205 LYS cc_start: 0.8216 (tttt) cc_final: 0.7877 (tttp)
REVERT: C  234 LYS cc_start: 0.6760 (mmtt) cc_final: 0.6248 (pttt)
REVERT: C  259 MET cc_start: 0.7820 (mtm) cc_final: 0.7487 (mtp)
REVERT: C  274 LYS cc_start: 0.7926 (mttt) cc_final: 0.7613 (mttp)
REVERT: C  311 LYS cc_start: 0.7292 (mmpt) cc_final: 0.6640 (mmtt)
REVERT: C  329 LYS cc_start: 0.6605 (mtpt) cc_final: 0.5372 (mptm)
REVERT: C  423 TYR cc_start: 0.8402 (m-80) cc_final: 0.8001 (m-80)
REVERT: D  113 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7189 (mm-30)
REVERT: D  121 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8323 (pt)
REVERT: D  205 LYS cc_start: 0.8191 (tttt) cc_final: 0.7863 (tttp)
REVERT: D  230 GLU cc_start: 0.6971 (tt0) cc_final: 0.6546 (tm-30)
REVERT: D  234 LYS cc_start: 0.6543 (mmtt) cc_final: 0.5961 (mmpt)
REVERT: D  259 MET cc_start: 0.7808 (mtm) cc_final: 0.7482 (mtp)
REVERT: D  274 LYS cc_start: 0.7947 (mttt) cc_final: 0.7639 (mttp)
REVERT: D  311 LYS cc_start: 0.7295 (mmpt) cc_final: 0.6637 (mmtt)
REVERT: D  329 LYS cc_start: 0.6613 (mtpt) cc_final: 0.5385 (mptm)
REVERT: D  359 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7415 (pm20)
REVERT: D  423 TYR cc_start: 0.8407 (m-80) cc_final: 0.8010 (m-80)
  outliers start: 55
  outliers final: 11
  residues processed: 241
  average time/residue: 0.6616
  time to fit residues: 173.7070
Evaluate side-chains
  208 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  342 MET
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  342 MET
Chi-restraints excluded: chain D residue  359 GLU
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 162 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 113 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 124 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 339 ASN
B  37 GLN
B 255 HIS
B 339 ASN
C  37 GLN
C 255 HIS
C 339 ASN
D  37 GLN
D 255 HIS
D 339 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.160116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.123051 restraints weight = 14282.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.02
r_work: 0.3255 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13472  Z= 0.131
  Angle     :  0.528   4.980  18328  Z= 0.277
  Chirality :  0.042   0.139   1948
  Planarity :  0.004   0.042   2344
  Dihedral  :  4.159  16.231   1780
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 12.54 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.21), residues: 1632
  helix:  0.65 (0.19), residues: 692
  sheet: -1.49 (0.28), residues: 344
  loop : -0.06 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 331 
 TYR   0.020   0.001   TYR B 264 
 PHE   0.011   0.001   PHE B 248 
 TRP   0.009   0.001   TRP D  27 
 HIS   0.004   0.001   HIS D  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13472)
  covalent geometry    : angle       0.52766 (18328)
  hydrogen bonds       : bond        0.03227 (  728)
  hydrogen bonds       : angle       5.62456 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 199
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7172 (mm-30)
REVERT: A  121 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8375 (pt)
REVERT: A  205 LYS cc_start: 0.8245 (tttt) cc_final: 0.7917 (tttp)
REVERT: A  230 GLU cc_start: 0.7028 (tt0) cc_final: 0.6602 (tm-30)
REVERT: A  234 LYS cc_start: 0.6612 (mmtt) cc_final: 0.6067 (mmpt)
REVERT: A  259 MET cc_start: 0.7821 (mtm) cc_final: 0.7500 (mtp)
REVERT: A  274 LYS cc_start: 0.7971 (mttt) cc_final: 0.7662 (mttp)
REVERT: A  311 LYS cc_start: 0.7372 (mmpt) cc_final: 0.6668 (mmtt)
REVERT: A  329 LYS cc_start: 0.6689 (mtpt) cc_final: 0.5338 (mptm)
REVERT: A  423 TYR cc_start: 0.8476 (m-80) cc_final: 0.8141 (m-80)
REVERT: B  113 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7319 (mm-30)
REVERT: B  121 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8340 (pt)
REVERT: B  205 LYS cc_start: 0.8231 (tttt) cc_final: 0.7886 (tttp)
REVERT: B  234 LYS cc_start: 0.6675 (mmtt) cc_final: 0.6097 (mtpp)
REVERT: B  259 MET cc_start: 0.7826 (mtm) cc_final: 0.7489 (mtp)
REVERT: B  274 LYS cc_start: 0.8037 (mttt) cc_final: 0.7730 (mttp)
REVERT: B  311 LYS cc_start: 0.7361 (mmpt) cc_final: 0.6660 (mmtt)
REVERT: B  329 LYS cc_start: 0.6713 (mtpt) cc_final: 0.5346 (mptm)
REVERT: B  423 TYR cc_start: 0.8484 (m-80) cc_final: 0.8185 (m-80)
REVERT: C  113 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7185 (mm-30)
REVERT: C  121 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8385 (pt)
REVERT: C  205 LYS cc_start: 0.8236 (tttt) cc_final: 0.7906 (tttp)
REVERT: C  230 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6851 (tm-30)
REVERT: C  259 MET cc_start: 0.7839 (mtm) cc_final: 0.7516 (mtp)
REVERT: C  274 LYS cc_start: 0.7966 (mttt) cc_final: 0.7657 (mttp)
REVERT: C  311 LYS cc_start: 0.7361 (mmpt) cc_final: 0.6660 (mmtt)
REVERT: C  329 LYS cc_start: 0.6742 (mtpt) cc_final: 0.5428 (mptm)
REVERT: C  423 TYR cc_start: 0.8481 (m-80) cc_final: 0.8207 (m-80)
REVERT: D  113 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7163 (mm-30)
REVERT: D  121 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8390 (pt)
REVERT: D  205 LYS cc_start: 0.8239 (tttt) cc_final: 0.7907 (tttp)
REVERT: D  234 LYS cc_start: 0.6612 (mmtt) cc_final: 0.6035 (mtpp)
REVERT: D  259 MET cc_start: 0.7830 (mtm) cc_final: 0.7506 (mtp)
REVERT: D  274 LYS cc_start: 0.7984 (mttt) cc_final: 0.7678 (mttp)
REVERT: D  311 LYS cc_start: 0.7362 (mmpt) cc_final: 0.6665 (mmtt)
REVERT: D  329 LYS cc_start: 0.6704 (mtpt) cc_final: 0.5362 (mptm)
REVERT: D  423 TYR cc_start: 0.8483 (m-80) cc_final: 0.8148 (m-80)
  outliers start: 48
  outliers final: 22
  residues processed: 224
  average time/residue: 0.6944
  time to fit residues: 168.6793
Evaluate side-chains
  217 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 187
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain C residue  354 TYR
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  354 TYR
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 115 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 146 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
A 339 ASN
B 255 HIS
B 339 ASN
C 255 HIS
C 339 ASN
D 255 HIS
D 339 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.161870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125236 restraints weight = 14344.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.03
r_work: 0.3268 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13472  Z= 0.114
  Angle     :  0.513   4.983  18328  Z= 0.270
  Chirality :  0.042   0.140   1948
  Planarity :  0.005   0.045   2344
  Dihedral  :  4.117  15.994   1780
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.10 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.21), residues: 1632
  helix:  0.78 (0.19), residues: 688
  sheet: -1.44 (0.28), residues: 344
  loop : -0.07 (0.27), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 331 
 TYR   0.019   0.001   TYR B 264 
 PHE   0.011   0.001   PHE D 248 
 TRP   0.008   0.001   TRP D  27 
 HIS   0.003   0.001   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (13472)
  covalent geometry    : angle       0.51310 (18328)
  hydrogen bonds       : bond        0.03095 (  728)
  hydrogen bonds       : angle       5.56078 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 205
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7145 (mm-30)
REVERT: A  205 LYS cc_start: 0.8227 (tttt) cc_final: 0.7912 (tttp)
REVERT: A  230 GLU cc_start: 0.7034 (tt0) cc_final: 0.6519 (tm-30)
REVERT: A  234 LYS cc_start: 0.6639 (mmtt) cc_final: 0.6098 (mmpt)
REVERT: A  259 MET cc_start: 0.7816 (mtm) cc_final: 0.7503 (mtp)
REVERT: A  274 LYS cc_start: 0.7987 (mttt) cc_final: 0.7684 (mttp)
REVERT: A  311 LYS cc_start: 0.7366 (mmpt) cc_final: 0.6656 (mmtt)
REVERT: A  329 LYS cc_start: 0.6685 (mtpt) cc_final: 0.5457 (mptm)
REVERT: A  423 TYR cc_start: 0.8442 (m-80) cc_final: 0.8132 (m-80)
REVERT: B  113 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7289 (mm-30)
REVERT: B  121 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8340 (pt)
REVERT: B  205 LYS cc_start: 0.8212 (tttt) cc_final: 0.7872 (tttp)
REVERT: B  230 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6776 (tm-30)
REVERT: B  259 MET cc_start: 0.7818 (mtm) cc_final: 0.7487 (mtp)
REVERT: B  274 LYS cc_start: 0.8026 (mttt) cc_final: 0.7726 (mttp)
REVERT: B  311 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6626 (mmtt)
REVERT: B  329 LYS cc_start: 0.6721 (mtpt) cc_final: 0.5617 (mptt)
REVERT: B  423 TYR cc_start: 0.8466 (m-80) cc_final: 0.8206 (m-80)
REVERT: C  113 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7142 (mm-30)
REVERT: C  205 LYS cc_start: 0.8227 (tttt) cc_final: 0.7901 (tttp)
REVERT: C  230 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6733 (tm-30)
REVERT: C  234 LYS cc_start: 0.6742 (mmpt) cc_final: 0.6220 (mmpt)
REVERT: C  259 MET cc_start: 0.7809 (mtm) cc_final: 0.7485 (mtp)
REVERT: C  274 LYS cc_start: 0.7969 (mttt) cc_final: 0.7663 (mttp)
REVERT: C  311 LYS cc_start: 0.7377 (mmpt) cc_final: 0.6673 (mmtt)
REVERT: C  329 LYS cc_start: 0.6718 (mtpt) cc_final: 0.5497 (mptm)
REVERT: D  113 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7124 (mm-30)
REVERT: D  205 LYS cc_start: 0.8219 (tttt) cc_final: 0.7906 (tttp)
REVERT: D  230 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6761 (tm-30)
REVERT: D  234 LYS cc_start: 0.6911 (mmtt) cc_final: 0.6675 (mmpt)
REVERT: D  259 MET cc_start: 0.7818 (mtm) cc_final: 0.7504 (mtp)
REVERT: D  274 LYS cc_start: 0.8044 (mttt) cc_final: 0.7736 (mttp)
REVERT: D  311 LYS cc_start: 0.7386 (mmpt) cc_final: 0.6683 (mmtt)
REVERT: D  329 LYS cc_start: 0.6705 (mtpt) cc_final: 0.5475 (mptm)
REVERT: D  423 TYR cc_start: 0.8450 (m-80) cc_final: 0.8141 (m-80)
  outliers start: 49
  outliers final: 25
  residues processed: 230
  average time/residue: 0.6543
  time to fit residues: 164.0887
Evaluate side-chains
  218 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  354 TYR
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  354 TYR
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 119 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 161 optimal weight:    8.9990
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    9.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
A 255 HIS
A 339 ASN
B 255 HIS
C 255 HIS
C 339 ASN
D  37 GLN
D 255 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.159097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.122815 restraints weight = 14231.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.92
r_work: 0.3259 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13472  Z= 0.145
  Angle     :  0.536   4.942  18328  Z= 0.281
  Chirality :  0.043   0.151   1948
  Planarity :  0.005   0.051   2344
  Dihedral  :  4.202  16.421   1780
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 13.80 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.21), residues: 1632
  helix:  0.70 (0.19), residues: 692
  sheet: -1.42 (0.28), residues: 344
  loop : -0.09 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 331 
 TYR   0.019   0.002   TYR B 264 
 PHE   0.012   0.001   PHE B 248 
 TRP   0.009   0.001   TRP B  27 
 HIS   0.004   0.001   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13472)
  covalent geometry    : angle       0.53607 (18328)
  hydrogen bonds       : bond        0.03295 (  728)
  hydrogen bonds       : angle       5.61622 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 195
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7121 (mm-30)
REVERT: A  205 LYS cc_start: 0.8122 (tttt) cc_final: 0.7823 (tttp)
REVERT: A  217 MET cc_start: 0.8358 (mtm) cc_final: 0.8059 (mtt)
REVERT: A  221 MET cc_start: 0.7661 (mmt) cc_final: 0.7259 (mmt)
REVERT: A  234 LYS cc_start: 0.6628 (mmtt) cc_final: 0.6048 (mtpp)
REVERT: A  259 MET cc_start: 0.7788 (mtm) cc_final: 0.7469 (mtp)
REVERT: A  274 LYS cc_start: 0.8148 (mttt) cc_final: 0.7810 (mttp)
REVERT: A  311 LYS cc_start: 0.7383 (mmpt) cc_final: 0.6667 (mmtt)
REVERT: A  329 LYS cc_start: 0.6661 (mtpt) cc_final: 0.5384 (mptm)
REVERT: A  423 TYR cc_start: 0.8535 (m-80) cc_final: 0.8275 (m-80)
REVERT: B  113 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7243 (mm-30)
REVERT: B  121 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (pt)
REVERT: B  205 LYS cc_start: 0.8118 (tttt) cc_final: 0.7816 (tttp)
REVERT: B  217 MET cc_start: 0.8323 (mtm) cc_final: 0.8015 (mtt)
REVERT: B  230 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6722 (tm-30)
REVERT: B  234 LYS cc_start: 0.6704 (mmpt) cc_final: 0.6226 (mmpt)
REVERT: B  259 MET cc_start: 0.7771 (mtm) cc_final: 0.7420 (mtp)
REVERT: B  274 LYS cc_start: 0.8037 (mttt) cc_final: 0.7726 (mttp)
REVERT: B  311 LYS cc_start: 0.7337 (mmpt) cc_final: 0.6656 (mmtt)
REVERT: B  329 LYS cc_start: 0.6707 (mtpt) cc_final: 0.5560 (mptt)
REVERT: B  423 TYR cc_start: 0.8538 (m-80) cc_final: 0.8260 (m-80)
REVERT: C  113 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7119 (mm-30)
REVERT: C  205 LYS cc_start: 0.8101 (tttt) cc_final: 0.7802 (tttp)
REVERT: C  217 MET cc_start: 0.8373 (mtm) cc_final: 0.8078 (mtt)
REVERT: C  221 MET cc_start: 0.7719 (mmt) cc_final: 0.7304 (mmt)
REVERT: C  230 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6629 (tm-30)
REVERT: C  234 LYS cc_start: 0.6705 (mmpt) cc_final: 0.6085 (mmpt)
REVERT: C  259 MET cc_start: 0.7782 (mtm) cc_final: 0.7449 (mtp)
REVERT: C  274 LYS cc_start: 0.8058 (mttt) cc_final: 0.7737 (mttp)
REVERT: C  311 LYS cc_start: 0.7375 (mmpt) cc_final: 0.6660 (mmtt)
REVERT: C  329 LYS cc_start: 0.6684 (mtpt) cc_final: 0.5568 (mptt)
REVERT: C  423 TYR cc_start: 0.8533 (m-80) cc_final: 0.8266 (m-80)
REVERT: D  113 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7094 (mm-30)
REVERT: D  205 LYS cc_start: 0.8122 (tttt) cc_final: 0.7819 (tttp)
REVERT: D  230 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6779 (tm-30)
REVERT: D  234 LYS cc_start: 0.6853 (mmtt) cc_final: 0.6535 (mmpt)
REVERT: D  259 MET cc_start: 0.7786 (mtm) cc_final: 0.7460 (mtp)
REVERT: D  274 LYS cc_start: 0.8110 (mttt) cc_final: 0.7786 (mttp)
REVERT: D  311 LYS cc_start: 0.7386 (mmpt) cc_final: 0.6671 (mmtt)
REVERT: D  329 LYS cc_start: 0.6664 (mtpt) cc_final: 0.5392 (mptm)
REVERT: D  423 TYR cc_start: 0.8540 (m-80) cc_final: 0.8280 (m-80)
  outliers start: 50
  outliers final: 31
  residues processed: 225
  average time/residue: 0.6142
  time to fit residues: 149.9863
Evaluate side-chains
  217 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 181
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  354 TYR
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  354 TYR
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 153 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 144 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
A 255 HIS
B 136 ASN
B 197 GLN
B 255 HIS
C 255 HIS
D 255 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.156077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.119936 restraints weight = 14358.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.83
r_work: 0.3201 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13472  Z= 0.216
  Angle     :  0.599   5.556  18328  Z= 0.315
  Chirality :  0.045   0.186   1948
  Planarity :  0.005   0.053   2344
  Dihedral  :  4.471  16.726   1780
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.80 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.21), residues: 1632
  helix:  0.51 (0.19), residues: 688
  sheet: -1.54 (0.27), residues: 352
  loop : -0.22 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 331 
 TYR   0.021   0.002   TYR D 264 
 PHE   0.014   0.002   PHE D 248 
 TRP   0.009   0.002   TRP D  27 
 HIS   0.006   0.001   HIS A  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (13472)
  covalent geometry    : angle       0.59927 (18328)
  hydrogen bonds       : bond        0.03737 (  728)
  hydrogen bonds       : angle       5.79716 ( 2076)

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

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

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3264 Ramachandran restraints generated.
    1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 203
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (mm-30)
REVERT: A  137 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7129 (pm20)
REVERT: A  217 MET cc_start: 0.8370 (mtm) cc_final: 0.8041 (mtt)
REVERT: A  234 LYS cc_start: 0.6821 (mmtt) cc_final: 0.6544 (mmtt)
REVERT: A  259 MET cc_start: 0.7762 (mtm) cc_final: 0.7525 (mtm)
REVERT: A  274 LYS cc_start: 0.8214 (mttt) cc_final: 0.7884 (mttp)
REVERT: A  311 LYS cc_start: 0.7213 (mmpt) cc_final: 0.6503 (mmtt)
REVERT: A  329 LYS cc_start: 0.6705 (mtpt) cc_final: 0.5416 (mptm)
REVERT: A  354 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7876 (m-10)
REVERT: B  113 GLU cc_start: 0.7664 (tt0) cc_final: 0.7292 (mm-30)
REVERT: B  217 MET cc_start: 0.8316 (mtm) cc_final: 0.7989 (mtt)
REVERT: B  230 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6563 (tm-30)
REVERT: B  234 LYS cc_start: 0.6657 (mmpt) cc_final: 0.6137 (mmpt)
REVERT: B  259 MET cc_start: 0.7738 (mtm) cc_final: 0.7481 (mtm)
REVERT: B  274 LYS cc_start: 0.8209 (mttt) cc_final: 0.7877 (mttp)
REVERT: B  311 LYS cc_start: 0.7208 (mmpt) cc_final: 0.6513 (mmtt)
REVERT: B  329 LYS cc_start: 0.6765 (mtpt) cc_final: 0.5471 (mptm)
REVERT: C  113 GLU cc_start: 0.7672 (tt0) cc_final: 0.7202 (mm-30)
REVERT: C  137 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7120 (pm20)
REVERT: C  234 LYS cc_start: 0.6718 (mmpt) cc_final: 0.6336 (mtpp)
REVERT: C  259 MET cc_start: 0.7749 (mtm) cc_final: 0.7355 (mtp)
REVERT: C  274 LYS cc_start: 0.8215 (mttt) cc_final: 0.7876 (mttp)
REVERT: C  311 LYS cc_start: 0.7208 (mmpt) cc_final: 0.6499 (mmtt)
REVERT: C  329 LYS cc_start: 0.6704 (mtpt) cc_final: 0.5455 (mptm)
REVERT: C  354 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7865 (m-10)
REVERT: D  113 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7188 (mm-30)
REVERT: D  137 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7135 (pm20)
REVERT: D  217 MET cc_start: 0.8333 (mtm) cc_final: 0.7996 (mtt)
REVERT: D  230 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6709 (tm-30)
REVERT: D  234 LYS cc_start: 0.6671 (mmtt) cc_final: 0.6305 (mmpt)
REVERT: D  259 MET cc_start: 0.7729 (mtm) cc_final: 0.7488 (mtm)
REVERT: D  274 LYS cc_start: 0.8224 (mttt) cc_final: 0.7893 (mttp)
REVERT: D  311 LYS cc_start: 0.7240 (mmpt) cc_final: 0.6531 (mmtt)
REVERT: D  329 LYS cc_start: 0.6708 (mtpt) cc_final: 0.5447 (mptm)
  outliers start: 51
  outliers final: 26
  residues processed: 235
  average time/residue: 0.5877
  time to fit residues: 150.5415
Evaluate side-chains
  224 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  121 ILE
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  137 GLU
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
Chi-restraints excluded: chain C residue  354 TYR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  137 GLU
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  354 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1505 > 50:
  distance: 16 - 22:  30.610
  distance: 22 - 23:   8.086
  distance: 23 - 24:  39.860
  distance: 23 - 26:  43.947
  distance: 24 - 25:  41.116
  distance: 24 - 28:  10.103
  distance: 26 - 27:  28.154
  distance: 28 - 29:  38.654
  distance: 29 - 30:  23.422
  distance: 29 - 32:  40.983
  distance: 30 - 31:  59.988
  distance: 30 - 37:  36.348
  distance: 32 - 33:  24.345
  distance: 33 - 34:  11.758
  distance: 34 - 35:  28.990
  distance: 35 - 36:  44.158
  distance: 37 - 38:  22.545
  distance: 38 - 39:  26.848
  distance: 38 - 41:  54.333
  distance: 39 - 40:  46.247
  distance: 39 - 46:  25.068
  distance: 41 - 42:  47.216
  distance: 42 - 43:  33.636
  distance: 43 - 44:  43.849
  distance: 46 - 47:   4.743
  distance: 47 - 48:  41.445
  distance: 47 - 50:  46.770
  distance: 48 - 49:  19.487
  distance: 48 - 54:  21.242
  distance: 49 - 65:  59.859
  distance: 50 - 51:  13.571
  distance: 51 - 52:  30.519
  distance: 51 - 53:  41.134
  distance: 54 - 55:  38.110
  distance: 54 - 60:  20.191
  distance: 55 - 56:  42.313
  distance: 55 - 58:  46.711
  distance: 56 - 57:  24.420
  distance: 56 - 61:  16.523
  distance: 58 - 59:  48.618
  distance: 59 - 60:  37.329
  distance: 61 - 62:  27.359
  distance: 63 - 65:  22.298
  distance: 65 - 66:  19.358
  distance: 66 - 67:  58.186
  distance: 67 - 68:  20.465
  distance: 67 - 69:   9.554
  distance: 69 - 70:  19.560
  distance: 70 - 71:  14.578
  distance: 70 - 73:  34.524
  distance: 71 - 72:  29.206
  distance: 71 - 78:  24.183
  distance: 73 - 74:  43.008
  distance: 74 - 75:  46.868
  distance: 75 - 76:  40.694
  distance: 76 - 77:  38.322
  distance: 78 - 79:  12.014
  distance: 79 - 80:  22.781
  distance: 79 - 82:  52.780
  distance: 80 - 81:  42.204
  distance: 80 - 87:  33.978
  distance: 82 - 83:  55.372
  distance: 83 - 84:  19.192
  distance: 84 - 85:  35.350
  distance: 84 - 86:  20.468
  distance: 87 - 88:   3.063
  distance: 88 - 89:  27.045
  distance: 88 - 91:   3.253
  distance: 89 - 90:  23.893
  distance: 89 - 98:  21.507
  distance: 91 - 92:  43.340
  distance: 92 - 93:  16.346
  distance: 93 - 94:  21.530
  distance: 94 - 95:  30.745
  distance: 95 - 96:  35.631
  distance: 95 - 97:  26.943