Starting phenix.real_space_refine
on Wed Jul 30 23:05:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9e_39075/07_2025/8y9e_39075.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9e_39075/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y9e_39075/07_2025/8y9e_39075.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9e_39075/07_2025/8y9e_39075.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9e_39075/07_2025/8y9e_39075.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9e_39075/07_2025/8y9e_39075.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, D
  Time building chain proxies: 6.63, per 1000 atoms: 0.51
  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: 3.31
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  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: 1.44
  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: 6.26

  Time building geometry restraints manager: 3.79 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             0.640
  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:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.860
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.060
  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:17.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.800
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.86 (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
 TRP   0.012   0.002   TRP D  27 
 HIS   0.005   0.001   HIS B  38 
 PHE   0.011   0.001   PHE A 310 
 TYR   0.014   0.002   TYR B 280 
 ARG   0.002   0.000   ARG A  43 

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

*********************** 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  : 1.516 
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: 1.3670
  time to fit residues: 388.5492
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  : 1.447 
-------------------------------------------------------------------------------
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 138 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.159486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122827 restraints weight = 14051.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.88
r_work: 0.3274 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13472  Z= 0.144
  Angle     :  0.557   4.880  18328  Z= 0.293
  Chirality :  0.044   0.156   1948
  Planarity :  0.004   0.044   2344
  Dihedral  :  4.547  16.546   1788
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  8.73 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.20), residues: 1632
  helix: -0.61 (0.18), residues: 720
  sheet: -1.57 (0.28), residues: 340
  loop : -1.05 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  27 
 HIS   0.004   0.001   HIS A  38 
 PHE   0.012   0.001   PHE B 248 
 TYR   0.024   0.002   TYR B 264 
 ARG   0.003   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03800 (  728)
  hydrogen bonds       : angle       6.05243 ( 2076)
  covalent geometry    : bond        0.00342 (13472)
  covalent geometry    : angle       0.55708 (18328)

*********************** 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: 36
    poor density    : 235
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7462 (mm-30)
REVERT: A  205 LYS cc_start: 0.8170 (tttt) cc_final: 0.7808 (tttp)
REVERT: A  234 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6861 (mtpp)
REVERT: A  259 MET cc_start: 0.7777 (mtm) cc_final: 0.7559 (mtm)
REVERT: A  311 LYS cc_start: 0.7418 (mmpt) cc_final: 0.6802 (mmpt)
REVERT: A  329 LYS cc_start: 0.6594 (mtpt) cc_final: 0.5338 (mptm)
REVERT: A  423 TYR cc_start: 0.8388 (m-80) cc_final: 0.8071 (m-80)
REVERT: B  113 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7468 (mm-30)
REVERT: B  196 MET cc_start: 0.8123 (mmm) cc_final: 0.7658 (mmt)
REVERT: B  205 LYS cc_start: 0.8183 (tttt) cc_final: 0.7829 (tttp)
REVERT: B  234 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6950 (mtpp)
REVERT: B  259 MET cc_start: 0.7763 (mtm) cc_final: 0.7426 (mtp)
REVERT: B  311 LYS cc_start: 0.7422 (mmpt) cc_final: 0.6805 (mmpt)
REVERT: B  329 LYS cc_start: 0.6716 (mtpt) cc_final: 0.5463 (mptm)
REVERT: C  113 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7454 (mm-30)
REVERT: C  205 LYS cc_start: 0.8176 (tttt) cc_final: 0.7802 (tttp)
REVERT: C  234 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6886 (mtpp)
REVERT: C  259 MET cc_start: 0.7771 (mtm) cc_final: 0.7553 (mtm)
REVERT: C  311 LYS cc_start: 0.7430 (mmpt) cc_final: 0.6818 (mmpt)
REVERT: C  329 LYS cc_start: 0.6586 (mtpt) cc_final: 0.5325 (mptm)
REVERT: D  113 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7468 (mm-30)
REVERT: D  205 LYS cc_start: 0.8156 (tttt) cc_final: 0.7795 (tttp)
REVERT: D  234 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6861 (mtpp)
REVERT: D  259 MET cc_start: 0.7767 (mtm) cc_final: 0.7546 (mtm)
REVERT: D  311 LYS cc_start: 0.7411 (mmpt) cc_final: 0.6798 (mmpt)
REVERT: D  329 LYS cc_start: 0.6614 (mtpt) cc_final: 0.5377 (mptm)
REVERT: D  423 TYR cc_start: 0.8371 (m-80) cc_final: 0.8131 (m-80)
  outliers start: 36
  outliers final: 16
  residues processed: 252
  average time/residue: 1.2791
  time to fit residues: 350.7337
Evaluate side-chains
  213 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 193
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
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 43 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0770
   chunk 105 optimal weight:   10.0000
   chunk 144 optimal weight:    9.9990
   chunk 141 optimal weight:    3.9990
   chunk 135 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.4144

-------------------------------------------------------------------------------
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
B 334 ASN
C 255 HIS
C 334 ASN
D 255 HIS
D 334 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.157798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121090 restraints weight = 14279.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.90
r_work: 0.3233 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2304

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= 0.162
  Angle     :  0.562   4.882  18328  Z= 0.295
  Chirality :  0.044   0.143   1948
  Planarity :  0.005   0.042   2344
  Dihedral  :  4.425  16.102   1780
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 11.55 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.21), residues: 1632
  helix: -0.09 (0.18), residues: 720
  sheet: -1.50 (0.28), residues: 348
  loop : -0.62 (0.27), residues: 564

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  728)
  hydrogen bonds       : angle       5.86931 ( 2076)
  covalent geometry    : bond        0.00393 (13472)
  covalent geometry    : angle       0.56179 (18328)

*********************** 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
  258 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 211
  time to evaluate  : 1.354 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7797 (tt0) cc_final: 0.7476 (mm-30)
REVERT: A  205 LYS cc_start: 0.8140 (tttt) cc_final: 0.7846 (tttp)
REVERT: A  230 GLU cc_start: 0.6991 (tt0) cc_final: 0.6395 (tm-30)
REVERT: A  234 LYS cc_start: 0.6884 (mmtt) cc_final: 0.6488 (mmpt)
REVERT: A  259 MET cc_start: 0.7785 (mtm) cc_final: 0.7413 (mtp)
REVERT: A  274 LYS cc_start: 0.8106 (mttt) cc_final: 0.7796 (mttp)
REVERT: A  311 LYS cc_start: 0.7390 (mmpt) cc_final: 0.6717 (mmtt)
REVERT: A  329 LYS cc_start: 0.6582 (mtpt) cc_final: 0.5292 (mptm)
REVERT: A  359 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7437 (pm20)
REVERT: B  113 GLU cc_start: 0.7798 (tt0) cc_final: 0.7471 (mm-30)
REVERT: B  205 LYS cc_start: 0.8185 (tttt) cc_final: 0.7896 (tttp)
REVERT: B  234 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6706 (mtpp)
REVERT: B  259 MET cc_start: 0.7778 (mtm) cc_final: 0.7387 (mtp)
REVERT: B  274 LYS cc_start: 0.8030 (mttt) cc_final: 0.7693 (mttp)
REVERT: B  311 LYS cc_start: 0.7368 (mmpt) cc_final: 0.6698 (mmtt)
REVERT: B  329 LYS cc_start: 0.6718 (mtpt) cc_final: 0.5428 (mptm)
REVERT: B  354 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8102 (m-10)
REVERT: B  359 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7439 (pm20)
REVERT: C  113 GLU cc_start: 0.7785 (tt0) cc_final: 0.7458 (mm-30)
REVERT: C  205 LYS cc_start: 0.8131 (tttt) cc_final: 0.7837 (tttp)
REVERT: C  230 GLU cc_start: 0.7011 (tt0) cc_final: 0.6424 (tm-30)
REVERT: C  234 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6437 (mmpt)
REVERT: C  259 MET cc_start: 0.7767 (mtm) cc_final: 0.7378 (mtp)
REVERT: C  274 LYS cc_start: 0.8023 (mttt) cc_final: 0.7681 (mttp)
REVERT: C  311 LYS cc_start: 0.7377 (mmpt) cc_final: 0.6705 (mmtt)
REVERT: C  329 LYS cc_start: 0.6586 (mtpt) cc_final: 0.5310 (mptm)
REVERT: C  359 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7410 (pm20)
REVERT: D  113 GLU cc_start: 0.7794 (tt0) cc_final: 0.7449 (mm-30)
REVERT: D  205 LYS cc_start: 0.8175 (tttt) cc_final: 0.7883 (tttp)
REVERT: D  230 GLU cc_start: 0.6997 (tt0) cc_final: 0.6416 (tm-30)
REVERT: D  234 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6443 (mmpt)
REVERT: D  259 MET cc_start: 0.7779 (mtm) cc_final: 0.7400 (mtp)
REVERT: D  274 LYS cc_start: 0.8067 (mttt) cc_final: 0.7726 (mttp)
REVERT: D  311 LYS cc_start: 0.7376 (mmpt) cc_final: 0.6700 (mmtt)
REVERT: D  329 LYS cc_start: 0.6588 (mtpt) cc_final: 0.5320 (mptm)
REVERT: D  359 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7407 (pm20)
  outliers start: 47
  outliers final: 22
  residues processed: 243
  average time/residue: 1.2174
  time to fit residues: 322.4874
Evaluate side-chains
  206 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 179
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
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  318 ASP
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  325 LEU
Chi-restraints excluded: chain B residue  342 MET
Chi-restraints excluded: chain B residue  354 TYR
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  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  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 21 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 142 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 95 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.160001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.122648 restraints weight = 14105.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.02
r_work: 0.3252 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13472  Z= 0.126
  Angle     :  0.528   4.886  18328  Z= 0.278
  Chirality :  0.043   0.142   1948
  Planarity :  0.005   0.043   2344
  Dihedral  :  4.297  16.281   1780
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.75 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.21), residues: 1632
  helix:  0.16 (0.19), residues: 720
  sheet: -1.50 (0.28), residues: 348
  loop : -0.44 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  27 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.009   0.001   PHE B 310 
 TYR   0.021   0.001   TYR C 264 
 ARG   0.005   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  728)
  hydrogen bonds       : angle       5.73344 ( 2076)
  covalent geometry    : bond        0.00299 (13472)
  covalent geometry    : angle       0.52796 (18328)

*********************** 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
  248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 199
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7776 (tt0) cc_final: 0.7424 (mm-30)
REVERT: A  121 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8323 (pt)
REVERT: A  205 LYS cc_start: 0.8239 (tttt) cc_final: 0.7906 (tttp)
REVERT: A  230 GLU cc_start: 0.6996 (tt0) cc_final: 0.6448 (tm-30)
REVERT: A  234 LYS cc_start: 0.6665 (mmtt) cc_final: 0.6093 (mmpt)
REVERT: A  259 MET cc_start: 0.7839 (mtm) cc_final: 0.7499 (mtp)
REVERT: A  274 LYS cc_start: 0.8070 (mttt) cc_final: 0.7753 (mttp)
REVERT: A  311 LYS cc_start: 0.7318 (mmpt) cc_final: 0.6650 (mmtt)
REVERT: A  329 LYS cc_start: 0.6652 (mtpt) cc_final: 0.5387 (mptm)
REVERT: A  359 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7486 (pm20)
REVERT: A  423 TYR cc_start: 0.8466 (m-80) cc_final: 0.8133 (m-80)
REVERT: B  113 GLU cc_start: 0.7745 (tt0) cc_final: 0.7472 (mm-30)
REVERT: B  205 LYS cc_start: 0.8243 (tttt) cc_final: 0.7901 (tttp)
REVERT: B  230 GLU cc_start: 0.7035 (tt0) cc_final: 0.6715 (tm-30)
REVERT: B  234 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6797 (mmtt)
REVERT: B  259 MET cc_start: 0.7837 (mtm) cc_final: 0.7453 (mtp)
REVERT: B  274 LYS cc_start: 0.8043 (mttt) cc_final: 0.7723 (mttp)
REVERT: B  311 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6668 (mmtt)
REVERT: B  329 LYS cc_start: 0.6654 (mtpt) cc_final: 0.5379 (mptm)
REVERT: B  359 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7469 (pm20)
REVERT: C  113 GLU cc_start: 0.7778 (tt0) cc_final: 0.7398 (mm-30)
REVERT: C  121 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8308 (pt)
REVERT: C  205 LYS cc_start: 0.8240 (tttt) cc_final: 0.7908 (tttp)
REVERT: C  230 GLU cc_start: 0.7007 (tt0) cc_final: 0.6483 (tm-30)
REVERT: C  234 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6428 (mmpt)
REVERT: C  259 MET cc_start: 0.7831 (mtm) cc_final: 0.7476 (mtp)
REVERT: C  274 LYS cc_start: 0.8077 (mttt) cc_final: 0.7778 (mttp)
REVERT: C  311 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6652 (mmtt)
REVERT: C  329 LYS cc_start: 0.6647 (mtpt) cc_final: 0.5387 (mptm)
REVERT: C  354 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8121 (m-10)
REVERT: C  359 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7474 (pm20)
REVERT: D  113 GLU cc_start: 0.7796 (tt0) cc_final: 0.7427 (mm-30)
REVERT: D  121 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8333 (pt)
REVERT: D  205 LYS cc_start: 0.8233 (tttt) cc_final: 0.7905 (tttp)
REVERT: D  230 GLU cc_start: 0.6985 (tt0) cc_final: 0.6451 (tm-30)
REVERT: D  234 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6406 (mmpt)
REVERT: D  259 MET cc_start: 0.7830 (mtm) cc_final: 0.7484 (mtp)
REVERT: D  274 LYS cc_start: 0.8072 (mttt) cc_final: 0.7778 (mttp)
REVERT: D  311 LYS cc_start: 0.7331 (mmpt) cc_final: 0.6656 (mmtt)
REVERT: D  329 LYS cc_start: 0.6624 (mtpt) cc_final: 0.5374 (mptm)
REVERT: D  359 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7453 (pm20)
REVERT: D  423 TYR cc_start: 0.8462 (m-80) cc_final: 0.8132 (m-80)
  outliers start: 49
  outliers final: 17
  residues processed: 232
  average time/residue: 1.3613
  time to fit residues: 342.2914
Evaluate side-chains
  199 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 174
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
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  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  121 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  121 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  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  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 153 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 158 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 129 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 123 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 339 ASN
C 255 HIS
C 339 ASN
D 255 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.157798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121075 restraints weight = 14377.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.91
r_work: 0.3227 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13472  Z= 0.157
  Angle     :  0.549   4.977  18328  Z= 0.288
  Chirality :  0.043   0.143   1948
  Planarity :  0.005   0.040   2344
  Dihedral  :  4.316  16.631   1780
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 12.89 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.21), residues: 1632
  helix:  0.39 (0.19), residues: 692
  sheet: -1.54 (0.28), residues: 348
  loop : -0.11 (0.28), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  27 
 HIS   0.004   0.001   HIS A  69 
 PHE   0.011   0.001   PHE A 310 
 TYR   0.021   0.002   TYR C 264 
 ARG   0.007   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03463 (  728)
  hydrogen bonds       : angle       5.74852 ( 2076)
  covalent geometry    : bond        0.00381 (13472)
  covalent geometry    : angle       0.54921 (18328)

*********************** 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
  252 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 202
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7773 (tt0) cc_final: 0.7363 (mm-30)
REVERT: A  121 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8304 (pt)
REVERT: A  205 LYS cc_start: 0.8125 (tttt) cc_final: 0.7829 (tttp)
REVERT: A  230 GLU cc_start: 0.6977 (tt0) cc_final: 0.6405 (tm-30)
REVERT: A  234 LYS cc_start: 0.6796 (mmtt) cc_final: 0.6375 (mmpt)
REVERT: A  259 MET cc_start: 0.7776 (mtm) cc_final: 0.7323 (mtp)
REVERT: A  274 LYS cc_start: 0.8078 (mttt) cc_final: 0.7784 (mttp)
REVERT: A  311 LYS cc_start: 0.7314 (mmpt) cc_final: 0.6619 (mmtt)
REVERT: A  329 LYS cc_start: 0.6610 (mtpt) cc_final: 0.5338 (mptm)
REVERT: A  359 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7457 (pm20)
REVERT: A  423 TYR cc_start: 0.8564 (m-80) cc_final: 0.8263 (m-80)
REVERT: B  113 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7335 (mm-30)
REVERT: B  205 LYS cc_start: 0.8129 (tttt) cc_final: 0.7819 (tttp)
REVERT: B  230 GLU cc_start: 0.7012 (tt0) cc_final: 0.6425 (tm-30)
REVERT: B  234 LYS cc_start: 0.6828 (mmtt) cc_final: 0.6412 (mmpt)
REVERT: B  259 MET cc_start: 0.7813 (mtm) cc_final: 0.7419 (mtp)
REVERT: B  274 LYS cc_start: 0.8092 (mttt) cc_final: 0.7781 (mttp)
REVERT: B  311 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6606 (mmtt)
REVERT: B  329 LYS cc_start: 0.6784 (mtpt) cc_final: 0.5413 (mptm)
REVERT: B  359 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7464 (pm20)
REVERT: C  113 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7358 (mm-30)
REVERT: C  121 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8280 (pt)
REVERT: C  205 LYS cc_start: 0.8124 (tttt) cc_final: 0.7829 (tttp)
REVERT: C  230 GLU cc_start: 0.7005 (tt0) cc_final: 0.6440 (tm-30)
REVERT: C  234 LYS cc_start: 0.6821 (mmtt) cc_final: 0.6407 (mmpt)
REVERT: C  259 MET cc_start: 0.7800 (mtm) cc_final: 0.7427 (mtp)
REVERT: C  274 LYS cc_start: 0.8062 (mttt) cc_final: 0.7765 (mttp)
REVERT: C  311 LYS cc_start: 0.7318 (mmpt) cc_final: 0.6652 (mmtt)
REVERT: C  329 LYS cc_start: 0.6661 (mtpt) cc_final: 0.5398 (mptm)
REVERT: D  113 GLU cc_start: 0.7783 (tt0) cc_final: 0.7338 (mm-30)
REVERT: D  121 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8300 (pt)
REVERT: D  205 LYS cc_start: 0.8122 (tttt) cc_final: 0.7826 (tttp)
REVERT: D  230 GLU cc_start: 0.6966 (tt0) cc_final: 0.6419 (tm-30)
REVERT: D  234 LYS cc_start: 0.6810 (mmtt) cc_final: 0.6392 (mmpt)
REVERT: D  259 MET cc_start: 0.7761 (mtm) cc_final: 0.7305 (mtp)
REVERT: D  274 LYS cc_start: 0.8079 (mttt) cc_final: 0.7785 (mttp)
REVERT: D  311 LYS cc_start: 0.7329 (mmpt) cc_final: 0.6655 (mmtt)
REVERT: D  329 LYS cc_start: 0.6589 (mtpt) cc_final: 0.5327 (mptm)
REVERT: D  423 TYR cc_start: 0.8555 (m-80) cc_final: 0.8260 (m-80)
  outliers start: 50
  outliers final: 24
  residues processed: 231
  average time/residue: 1.3166
  time to fit residues: 333.5435
Evaluate side-chains
  219 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
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  359 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain B residue   81 MET
Chi-restraints excluded: chain B residue   92 ILE
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  325 LEU
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  359 GLU
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  318 ASP
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 D residue   81 MET
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  318 ASP
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
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 19 optimal weight:    0.8980
   chunk 162 optimal weight:    0.9980
   chunk 138 optimal weight:    0.9990
   chunk 123 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 119 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 151 optimal weight:    0.6980
   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 = 0.3815 r_free = 0.3815 target = 0.161139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124726 restraints weight = 14411.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.93
r_work: 0.3279 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2844

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= 0.114
  Angle     :  0.509   4.895  18328  Z= 0.268
  Chirality :  0.042   0.135   1948
  Planarity :  0.005   0.043   2344
  Dihedral  :  4.172  16.423   1780
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.10 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.21), residues: 1632
  helix:  0.59 (0.19), residues: 692
  sheet: -1.48 (0.27), residues: 344
  loop : -0.08 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  27 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.010   0.001   PHE D 310 
 TYR   0.020   0.001   TYR A 264 
 ARG   0.008   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  728)
  hydrogen bonds       : angle       5.59329 ( 2076)
  covalent geometry    : bond        0.00268 (13472)
  covalent geometry    : angle       0.50888 (18328)

*********************** 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
  268 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 216
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7175 (mm-30)
REVERT: A  121 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8320 (pt)
REVERT: A  205 LYS cc_start: 0.8197 (tttt) cc_final: 0.7867 (tttp)
REVERT: A  230 GLU cc_start: 0.6972 (tt0) cc_final: 0.6357 (tm-30)
REVERT: A  234 LYS cc_start: 0.6766 (mmtt) cc_final: 0.6356 (mmpt)
REVERT: A  248 PHE cc_start: 0.7814 (t80) cc_final: 0.7159 (t80)
REVERT: A  259 MET cc_start: 0.7797 (mtm) cc_final: 0.7465 (mtp)
REVERT: A  274 LYS cc_start: 0.8048 (mttt) cc_final: 0.7728 (mttp)
REVERT: A  311 LYS cc_start: 0.7359 (mmpt) cc_final: 0.6664 (mmtt)
REVERT: A  329 LYS cc_start: 0.6706 (mtpt) cc_final: 0.5422 (mptm)
REVERT: A  423 TYR cc_start: 0.8440 (m-80) cc_final: 0.8131 (m-80)
REVERT: B  113 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7177 (mm-30)
REVERT: B  121 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8287 (pt)
REVERT: B  205 LYS cc_start: 0.8203 (tttt) cc_final: 0.7869 (tttp)
REVERT: B  230 GLU cc_start: 0.6999 (tt0) cc_final: 0.6772 (tm-30)
REVERT: B  234 LYS cc_start: 0.6849 (mmtt) cc_final: 0.6301 (mtpp)
REVERT: B  259 MET cc_start: 0.7822 (mtm) cc_final: 0.7463 (mtp)
REVERT: B  274 LYS cc_start: 0.8053 (mttt) cc_final: 0.7730 (mttp)
REVERT: B  311 LYS cc_start: 0.7336 (mmpt) cc_final: 0.6627 (mmtt)
REVERT: B  329 LYS cc_start: 0.6755 (mtpt) cc_final: 0.5405 (mptm)
REVERT: C  113 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7190 (mm-30)
REVERT: C  121 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8299 (pt)
REVERT: C  205 LYS cc_start: 0.8205 (tttt) cc_final: 0.7867 (tttp)
REVERT: C  230 GLU cc_start: 0.7003 (tt0) cc_final: 0.6394 (tm-30)
REVERT: C  234 LYS cc_start: 0.6782 (mmtt) cc_final: 0.6375 (mmpt)
REVERT: C  259 MET cc_start: 0.7796 (mtm) cc_final: 0.7457 (mtp)
REVERT: C  274 LYS cc_start: 0.7978 (mttt) cc_final: 0.7662 (mttp)
REVERT: C  311 LYS cc_start: 0.7336 (mmpt) cc_final: 0.6631 (mmtt)
REVERT: C  329 LYS cc_start: 0.6718 (mtpt) cc_final: 0.5444 (mptm)
REVERT: D  113 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7187 (mm-30)
REVERT: D  121 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8332 (pt)
REVERT: D  205 LYS cc_start: 0.8194 (tttt) cc_final: 0.7861 (tttp)
REVERT: D  230 GLU cc_start: 0.6973 (tt0) cc_final: 0.6759 (tm-30)
REVERT: D  234 LYS cc_start: 0.6757 (mmtt) cc_final: 0.6205 (mtpp)
REVERT: D  248 PHE cc_start: 0.7813 (t80) cc_final: 0.7154 (t80)
REVERT: D  259 MET cc_start: 0.7805 (mtm) cc_final: 0.7482 (mtp)
REVERT: D  274 LYS cc_start: 0.8064 (mttt) cc_final: 0.7742 (mttp)
REVERT: D  311 LYS cc_start: 0.7349 (mmpt) cc_final: 0.6638 (mmtt)
REVERT: D  329 LYS cc_start: 0.6718 (mtpt) cc_final: 0.5460 (mptm)
REVERT: D  423 TYR cc_start: 0.8434 (m-80) cc_final: 0.8128 (m-80)
  outliers start: 52
  outliers final: 20
  residues processed: 243
  average time/residue: 1.2957
  time to fit residues: 343.0305
Evaluate side-chains
  219 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
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  121 ILE
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  320 ILE
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  318 ASP
Chi-restraints excluded: chain B residue  320 ILE
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  113 GLU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  318 ASP
Chi-restraints excluded: chain C residue  320 ILE
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  318 ASP
Chi-restraints excluded: chain D residue  320 ILE
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 31 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 162 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 123 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 156 optimal weight:    7.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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
C 255 HIS
C 339 ASN
D 255 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.159649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.123475 restraints weight = 14313.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.90
r_work: 0.3266 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2854

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= 0.130
  Angle     :  0.528   4.977  18328  Z= 0.277
  Chirality :  0.042   0.139   1948
  Planarity :  0.005   0.047   2344
  Dihedral  :  4.200  16.634   1780
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.10 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.21), residues: 1632
  helix:  0.69 (0.19), residues: 692
  sheet: -1.47 (0.27), residues: 344
  loop : -0.05 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  27 
 HIS   0.004   0.001   HIS B  69 
 PHE   0.010   0.001   PHE C 310 
 TYR   0.019   0.001   TYR B 264 
 ARG   0.010   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03214 (  728)
  hydrogen bonds       : angle       5.60394 ( 2076)
  covalent geometry    : bond        0.00310 (13472)
  covalent geometry    : angle       0.52776 (18328)

*********************** 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
  256 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 203
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7114 (mm-30)
REVERT: A  121 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8308 (pt)
REVERT: A  205 LYS cc_start: 0.8186 (tttt) cc_final: 0.7824 (tttp)
REVERT: A  230 GLU cc_start: 0.6951 (tt0) cc_final: 0.6403 (tm-30)
REVERT: A  234 LYS cc_start: 0.6749 (mmtt) cc_final: 0.6328 (mmpt)
REVERT: A  259 MET cc_start: 0.7766 (mtm) cc_final: 0.7444 (mtp)
REVERT: A  274 LYS cc_start: 0.8101 (mttt) cc_final: 0.7759 (mttp)
REVERT: A  311 LYS cc_start: 0.7366 (mmpt) cc_final: 0.6663 (mmtt)
REVERT: A  329 LYS cc_start: 0.6701 (mtpt) cc_final: 0.5410 (mptm)
REVERT: A  423 TYR cc_start: 0.8459 (m-80) cc_final: 0.8182 (m-80)
REVERT: B  113 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7138 (mm-30)
REVERT: B  121 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (pt)
REVERT: B  205 LYS cc_start: 0.8189 (tttt) cc_final: 0.7817 (tttp)
REVERT: B  234 LYS cc_start: 0.6778 (mmtt) cc_final: 0.6241 (mtpp)
REVERT: B  259 MET cc_start: 0.7782 (mtm) cc_final: 0.7424 (mtp)
REVERT: B  274 LYS cc_start: 0.8068 (mttt) cc_final: 0.7741 (mttp)
REVERT: B  311 LYS cc_start: 0.7334 (mmpt) cc_final: 0.6621 (mmtt)
REVERT: B  329 LYS cc_start: 0.6736 (mtpt) cc_final: 0.5606 (mptt)
REVERT: C  113 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7119 (mm-30)
REVERT: C  121 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8268 (pt)
REVERT: C  205 LYS cc_start: 0.8184 (tttt) cc_final: 0.7810 (tttp)
REVERT: C  230 GLU cc_start: 0.6966 (tt0) cc_final: 0.6346 (tm-30)
REVERT: C  234 LYS cc_start: 0.6779 (mmtt) cc_final: 0.6356 (mmpt)
REVERT: C  259 MET cc_start: 0.7775 (mtm) cc_final: 0.7446 (mtp)
REVERT: C  274 LYS cc_start: 0.8103 (mttt) cc_final: 0.7758 (mttp)
REVERT: C  311 LYS cc_start: 0.7359 (mmpt) cc_final: 0.6652 (mmtt)
REVERT: C  329 LYS cc_start: 0.6696 (mtpt) cc_final: 0.5407 (mptm)
REVERT: D  113 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7116 (mm-30)
REVERT: D  121 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (pt)
REVERT: D  205 LYS cc_start: 0.8186 (tttt) cc_final: 0.7817 (tttp)
REVERT: D  230 GLU cc_start: 0.6963 (tt0) cc_final: 0.6717 (tm-30)
REVERT: D  234 LYS cc_start: 0.6752 (mmtt) cc_final: 0.6172 (mtpp)
REVERT: D  259 MET cc_start: 0.7763 (mtm) cc_final: 0.7442 (mtp)
REVERT: D  274 LYS cc_start: 0.8060 (mttt) cc_final: 0.7737 (mttp)
REVERT: D  311 LYS cc_start: 0.7364 (mmpt) cc_final: 0.6655 (mmtt)
REVERT: D  329 LYS cc_start: 0.6692 (mtpt) cc_final: 0.5409 (mptm)
REVERT: D  389 GLU cc_start: 0.7421 (tt0) cc_final: 0.6933 (tt0)
REVERT: D  423 TYR cc_start: 0.8454 (m-80) cc_final: 0.8177 (m-80)
  outliers start: 53
  outliers final: 28
  residues processed: 233
  average time/residue: 1.2704
  time to fit residues: 322.4305
Evaluate side-chains
  221 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
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  121 ILE
Chi-restraints excluded: chain A residue  318 ASP
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  318 ASP
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  121 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  318 ASP
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  325 LEU
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  121 ILE
Chi-restraints excluded: chain D residue  318 ASP
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 19 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 144 optimal weight:    6.9990
   chunk 130 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.160110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.124031 restraints weight = 14453.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.92
r_work: 0.3309 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13472  Z= 0.126
  Angle     :  0.528   6.044  18328  Z= 0.277
  Chirality :  0.042   0.148   1948
  Planarity :  0.005   0.043   2344
  Dihedral  :  4.187  16.522   1780
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.80 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.21), residues: 1632
  helix:  0.72 (0.19), residues: 692
  sheet: -1.41 (0.27), residues: 344
  loop : -0.06 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  27 
 HIS   0.004   0.001   HIS B  69 
 PHE   0.010   0.001   PHE C 310 
 TYR   0.019   0.001   TYR A 264 
 ARG   0.008   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (  728)
  hydrogen bonds       : angle       5.57160 ( 2076)
  covalent geometry    : bond        0.00301 (13472)
  covalent geometry    : angle       0.52822 (18328)

*********************** 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
  260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 213
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7130 (mm-30)
REVERT: A  205 LYS cc_start: 0.8189 (tttt) cc_final: 0.7828 (tttp)
REVERT: A  230 GLU cc_start: 0.6980 (tt0) cc_final: 0.6442 (tm-30)
REVERT: A  234 LYS cc_start: 0.6769 (mmtt) cc_final: 0.6428 (mmpt)
REVERT: A  259 MET cc_start: 0.7785 (mtm) cc_final: 0.7472 (mtp)
REVERT: A  274 LYS cc_start: 0.8054 (mttt) cc_final: 0.7724 (mttp)
REVERT: A  311 LYS cc_start: 0.7366 (mmpt) cc_final: 0.6658 (mmtt)
REVERT: A  329 LYS cc_start: 0.6698 (mtpt) cc_final: 0.5571 (mptt)
REVERT: A  423 TYR cc_start: 0.8455 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  113 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7130 (mm-30)
REVERT: B  121 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (pt)
REVERT: B  205 LYS cc_start: 0.8194 (tttt) cc_final: 0.7830 (tttp)
REVERT: B  230 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6855 (tm-30)
REVERT: B  259 MET cc_start: 0.7779 (mtm) cc_final: 0.7422 (mtp)
REVERT: B  274 LYS cc_start: 0.8074 (mttt) cc_final: 0.7749 (mttp)
REVERT: B  311 LYS cc_start: 0.7267 (mmpt) cc_final: 0.6494 (mmtt)
REVERT: B  329 LYS cc_start: 0.6729 (mtpt) cc_final: 0.5611 (mptt)
REVERT: C  113 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7144 (mm-30)
REVERT: C  121 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8312 (pt)
REVERT: C  205 LYS cc_start: 0.8191 (tttt) cc_final: 0.7829 (tttp)
REVERT: C  230 GLU cc_start: 0.6975 (tt0) cc_final: 0.6450 (tm-30)
REVERT: C  234 LYS cc_start: 0.6779 (mmtt) cc_final: 0.6440 (mmpt)
REVERT: C  259 MET cc_start: 0.7778 (mtm) cc_final: 0.7447 (mtp)
REVERT: C  274 LYS cc_start: 0.8039 (mttt) cc_final: 0.7702 (mttp)
REVERT: C  311 LYS cc_start: 0.7278 (mmpt) cc_final: 0.6502 (mmtt)
REVERT: C  329 LYS cc_start: 0.6693 (mtpt) cc_final: 0.5570 (mptt)
REVERT: D  113 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7127 (mm-30)
REVERT: D  205 LYS cc_start: 0.8194 (tttt) cc_final: 0.7832 (tttp)
REVERT: D  230 GLU cc_start: 0.6979 (tt0) cc_final: 0.6748 (tm-30)
REVERT: D  234 LYS cc_start: 0.6762 (mmtt) cc_final: 0.6192 (mtpp)
REVERT: D  259 MET cc_start: 0.7774 (mtm) cc_final: 0.7461 (mtp)
REVERT: D  274 LYS cc_start: 0.8044 (mttt) cc_final: 0.7712 (mttp)
REVERT: D  311 LYS cc_start: 0.7274 (mmpt) cc_final: 0.6495 (mmtt)
REVERT: D  329 LYS cc_start: 0.6684 (mtpt) cc_final: 0.5559 (mptt)
REVERT: D  423 TYR cc_start: 0.8468 (m-80) cc_final: 0.8196 (m-80)
  outliers start: 47
  outliers final: 30
  residues processed: 240
  average time/residue: 1.3154
  time to fit residues: 342.8177
Evaluate side-chains
  228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 192
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
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  265 LEU
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 LEU
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  318 ASP
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  121 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  318 ASP
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  265 LEU
Chi-restraints excluded: chain D residue  318 ASP
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  325 LEU
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 46 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 153 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 143 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.155786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.119539 restraints weight = 14351.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.83
r_work: 0.3201 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13472  Z= 0.215
  Angle     :  0.600   6.651  18328  Z= 0.313
  Chirality :  0.045   0.192   1948
  Planarity :  0.005   0.055   2344
  Dihedral  :  4.458  16.916   1780
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.51 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.21), residues: 1632
  helix:  0.51 (0.19), residues: 692
  sheet: -1.60 (0.27), residues: 352
  loop : -0.18 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  27 
 HIS   0.006   0.001   HIS D  69 
 PHE   0.010   0.002   PHE D 310 
 TYR   0.021   0.002   TYR B 264 
 ARG   0.012   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  728)
  hydrogen bonds       : angle       5.77139 ( 2076)
  covalent geometry    : bond        0.00530 (13472)
  covalent geometry    : angle       0.59960 (18328)

*********************** 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
  253 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 205
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7220 (mm-30)
REVERT: A  217 MET cc_start: 0.8352 (mtm) cc_final: 0.8018 (mtt)
REVERT: A  230 GLU cc_start: 0.7029 (tt0) cc_final: 0.6484 (tm-30)
REVERT: A  234 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6461 (mmpt)
REVERT: A  248 PHE cc_start: 0.7891 (t80) cc_final: 0.7222 (t80)
REVERT: A  259 MET cc_start: 0.7775 (mtm) cc_final: 0.7522 (mtm)
REVERT: A  274 LYS cc_start: 0.8247 (mttt) cc_final: 0.7885 (mttp)
REVERT: A  311 LYS cc_start: 0.7253 (mmpt) cc_final: 0.6551 (mmtt)
REVERT: A  329 LYS cc_start: 0.6789 (mtpt) cc_final: 0.5489 (mptm)
REVERT: B  113 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7238 (mm-30)
REVERT: B  217 MET cc_start: 0.8322 (mtm) cc_final: 0.7980 (mtt)
REVERT: B  230 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6793 (tm-30)
REVERT: B  234 LYS cc_start: 0.6777 (mmpt) cc_final: 0.6303 (mmpt)
REVERT: B  259 MET cc_start: 0.7750 (mtm) cc_final: 0.7527 (mtm)
REVERT: B  274 LYS cc_start: 0.8224 (mttt) cc_final: 0.7896 (mttp)
REVERT: B  311 LYS cc_start: 0.7233 (mmpt) cc_final: 0.6511 (mmtt)
REVERT: B  329 LYS cc_start: 0.6801 (mtpt) cc_final: 0.5658 (mptt)
REVERT: C  113 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7225 (mm-30)
REVERT: C  217 MET cc_start: 0.8336 (mtm) cc_final: 0.7996 (mtt)
REVERT: C  230 GLU cc_start: 0.7006 (tt0) cc_final: 0.6491 (tm-30)
REVERT: C  234 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6516 (mmpt)
REVERT: C  259 MET cc_start: 0.7772 (mtm) cc_final: 0.7379 (mtp)
REVERT: C  274 LYS cc_start: 0.8202 (mttt) cc_final: 0.7875 (mttp)
REVERT: C  311 LYS cc_start: 0.7223 (mmpt) cc_final: 0.6491 (mmtt)
REVERT: C  329 LYS cc_start: 0.6747 (mtpt) cc_final: 0.5465 (mptm)
REVERT: C  406 TYR cc_start: 0.8233 (m-80) cc_final: 0.7948 (m-80)
REVERT: D  113 GLU cc_start: 0.7709 (tt0) cc_final: 0.7228 (mm-30)
REVERT: D  217 MET cc_start: 0.8331 (mtm) cc_final: 0.7995 (mtt)
REVERT: D  230 GLU cc_start: 0.7029 (tt0) cc_final: 0.6826 (tm-30)
REVERT: D  234 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6310 (mtpp)
REVERT: D  248 PHE cc_start: 0.7893 (t80) cc_final: 0.7223 (t80)
REVERT: D  259 MET cc_start: 0.7761 (mtm) cc_final: 0.7506 (mtm)
REVERT: D  274 LYS cc_start: 0.8208 (mttt) cc_final: 0.7874 (mttp)
REVERT: D  311 LYS cc_start: 0.7266 (mmpt) cc_final: 0.6564 (mmtt)
REVERT: D  324 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6968 (pp20)
REVERT: D  329 LYS cc_start: 0.6754 (mtpt) cc_final: 0.5454 (mptm)
  outliers start: 48
  outliers final: 34
  residues processed: 234
  average time/residue: 1.1645
  time to fit residues: 298.7978
Evaluate side-chains
  226 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 188
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
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  318 ASP
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  325 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  318 ASP
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  106 SER
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  318 ASP
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  265 LEU
Chi-restraints excluded: chain D residue  318 ASP
Chi-restraints excluded: chain D residue  320 ILE
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 126 optimal weight:    0.8980
   chunk 127 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 141 optimal weight:    0.7980
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.159823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.124066 restraints weight = 14311.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.83
r_work: 0.3255 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13472  Z= 0.125
  Angle     :  0.537   6.420  18328  Z= 0.283
  Chirality :  0.042   0.155   1948
  Planarity :  0.005   0.049   2344
  Dihedral  :  4.292  17.250   1780
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.65 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1632
  helix:  0.62 (0.19), residues: 692
  sheet: -1.42 (0.27), residues: 344
  loop : -0.08 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 408 
 HIS   0.004   0.001   HIS D 385 
 PHE   0.009   0.001   PHE B 226 
 TYR   0.019   0.002   TYR A 264 
 ARG   0.011   0.001   ARG C 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  728)
  hydrogen bonds       : angle       5.62409 ( 2076)
  covalent geometry    : bond        0.00297 (13472)
  covalent geometry    : angle       0.53746 (18328)

********************** REFINEMENT MACRO_CYCLE 10 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: 42
    poor density    : 203
  time to evaluate  : 1.404 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7064 (mm-30)
REVERT: A  205 LYS cc_start: 0.8146 (tttt) cc_final: 0.7751 (tttp)
REVERT: A  217 MET cc_start: 0.8300 (mtm) cc_final: 0.7973 (mtt)
REVERT: A  230 GLU cc_start: 0.6909 (tt0) cc_final: 0.6355 (tm-30)
REVERT: A  234 LYS cc_start: 0.6820 (mmtt) cc_final: 0.6449 (mmpt)
REVERT: A  259 MET cc_start: 0.7731 (mtm) cc_final: 0.7505 (mtm)
REVERT: A  274 LYS cc_start: 0.8015 (mttt) cc_final: 0.7669 (mttp)
REVERT: A  311 LYS cc_start: 0.7193 (mmpt) cc_final: 0.6468 (mmtt)
REVERT: A  324 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6962 (pp20)
REVERT: A  329 LYS cc_start: 0.6753 (mtpt) cc_final: 0.5673 (mptt)
REVERT: A  423 TYR cc_start: 0.8392 (m-80) cc_final: 0.8060 (m-80)
REVERT: B  113 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7080 (mm-30)
REVERT: B  121 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8201 (pt)
REVERT: B  205 LYS cc_start: 0.8055 (tttt) cc_final: 0.7756 (tttp)
REVERT: B  217 MET cc_start: 0.8293 (mtm) cc_final: 0.7960 (mtt)
REVERT: B  234 LYS cc_start: 0.6516 (mmpt) cc_final: 0.6267 (pttt)
REVERT: B  259 MET cc_start: 0.7710 (mtm) cc_final: 0.7370 (mtp)
REVERT: B  274 LYS cc_start: 0.8116 (mttt) cc_final: 0.7792 (mttp)
REVERT: B  311 LYS cc_start: 0.7168 (mmpt) cc_final: 0.6450 (mmtt)
REVERT: B  329 LYS cc_start: 0.6763 (mtpt) cc_final: 0.5679 (mptt)
REVERT: B  406 TYR cc_start: 0.8077 (m-80) cc_final: 0.7622 (m-80)
REVERT: C  113 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7078 (mm-30)
REVERT: C  121 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8237 (pt)
REVERT: C  205 LYS cc_start: 0.8150 (tttt) cc_final: 0.7766 (tttp)
REVERT: C  217 MET cc_start: 0.8310 (mtm) cc_final: 0.7987 (mtt)
REVERT: C  230 GLU cc_start: 0.6913 (tt0) cc_final: 0.6380 (tm-30)
REVERT: C  234 LYS cc_start: 0.6838 (mmtt) cc_final: 0.6482 (mmpt)
REVERT: C  259 MET cc_start: 0.7719 (mtm) cc_final: 0.7483 (mtm)
REVERT: C  274 LYS cc_start: 0.8075 (mttt) cc_final: 0.7722 (mttp)
REVERT: C  311 LYS cc_start: 0.7191 (mmpt) cc_final: 0.6463 (mmtt)
REVERT: C  329 LYS cc_start: 0.6723 (mtpt) cc_final: 0.5645 (mptt)
REVERT: D  113 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7071 (mm-30)
REVERT: D  205 LYS cc_start: 0.8146 (tttt) cc_final: 0.7753 (tttp)
REVERT: D  217 MET cc_start: 0.8270 (mtm) cc_final: 0.7941 (mtt)
REVERT: D  234 LYS cc_start: 0.6825 (mmtt) cc_final: 0.6291 (mtpp)
REVERT: D  259 MET cc_start: 0.7716 (mtm) cc_final: 0.7482 (mtm)
REVERT: D  274 LYS cc_start: 0.8028 (mttt) cc_final: 0.7716 (mttp)
REVERT: D  311 LYS cc_start: 0.7183 (mmpt) cc_final: 0.6463 (mmtt)
REVERT: D  329 LYS cc_start: 0.6720 (mtpt) cc_final: 0.5639 (mptt)
REVERT: D  423 TYR cc_start: 0.8417 (m-80) cc_final: 0.7990 (m-80)
  outliers start: 42
  outliers final: 21
  residues processed: 224
  average time/residue: 1.3124
  time to fit residues: 320.8045
Evaluate side-chains
  212 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 184
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
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  113 GLU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  324 GLU
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  318 ASP
Chi-restraints excluded: chain B residue  320 ILE
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  113 GLU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  318 ASP
Chi-restraints excluded: chain C residue  320 ILE
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  265 LEU
Chi-restraints excluded: chain D residue  318 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 99 optimal weight:    0.4980
   chunk 104 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 124 optimal weight:    0.3980
   chunk 117 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0270
   chunk 41 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.162135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.126016 restraints weight = 14300.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.92
r_work: 0.3295 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3156

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= 0.109
  Angle     :  0.531   7.722  18328  Z= 0.278
  Chirality :  0.042   0.146   1948
  Planarity :  0.005   0.045   2344
  Dihedral  :  4.177  17.087   1780
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.21 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.21), residues: 1632
  helix:  0.80 (0.19), residues: 692
  sheet: -1.30 (0.28), residues: 344
  loop :  0.02 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 408 
 HIS   0.004   0.001   HIS C 385 
 PHE   0.011   0.001   PHE D 226 
 TYR   0.021   0.001   TYR D 354 
 ARG   0.010   0.001   ARG C 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03069 (  728)
  hydrogen bonds       : angle       5.53906 ( 2076)
  covalent geometry    : bond        0.00256 (13472)
  covalent geometry    : angle       0.53084 (18328)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10535.02 seconds
wall clock time: 181 minutes 16.10 seconds (10876.10 seconds total)