Starting phenix.real_space_refine
on Thu May 15 07:07:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9e_39075/05_2025/8y9e_39075.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9e_39075/05_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_39075/05_2025/8y9e_39075.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9e_39075/05_2025/8y9e_39075.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9e_39075/05_2025/8y9e_39075.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9e_39075/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.50, per 1000 atoms: 0.50
  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: 3.23
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.63
  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: 4.40

  Time building geometry restraints manager: 3.78 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: 0.09
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     29.930
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  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:10.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.830
-------------------------------------------------------------------------------
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  : 1.559 
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: 1.2503
  time to fit residues: 355.5345
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  : 1.361 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122826 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: 3.96 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
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  : 1.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7460 (mm-30)
REVERT: A  205 LYS cc_start: 0.8170 (tttt) cc_final: 0.7807 (tttp)
REVERT: A  234 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6860 (mtpp)
REVERT: A  259 MET cc_start: 0.7778 (mtm) cc_final: 0.7559 (mtm)
REVERT: A  311 LYS cc_start: 0.7417 (mmpt) cc_final: 0.6800 (mmpt)
REVERT: A  329 LYS cc_start: 0.6590 (mtpt) cc_final: 0.5334 (mptm)
REVERT: A  423 TYR cc_start: 0.8389 (m-80) cc_final: 0.8072 (m-80)
REVERT: B  113 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7467 (mm-30)
REVERT: B  196 MET cc_start: 0.8122 (mmm) cc_final: 0.7656 (mmt)
REVERT: B  205 LYS cc_start: 0.8184 (tttt) cc_final: 0.7829 (tttp)
REVERT: B  234 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6948 (mtpp)
REVERT: B  259 MET cc_start: 0.7763 (mtm) cc_final: 0.7425 (mtp)
REVERT: B  311 LYS cc_start: 0.7420 (mmpt) cc_final: 0.6803 (mmpt)
REVERT: B  329 LYS cc_start: 0.6713 (mtpt) cc_final: 0.5459 (mptm)
REVERT: C  113 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7453 (mm-30)
REVERT: C  205 LYS cc_start: 0.8176 (tttt) cc_final: 0.7803 (tttp)
REVERT: C  234 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6885 (mtpp)
REVERT: C  259 MET cc_start: 0.7771 (mtm) cc_final: 0.7552 (mtm)
REVERT: C  311 LYS cc_start: 0.7430 (mmpt) cc_final: 0.6817 (mmpt)
REVERT: C  329 LYS cc_start: 0.6581 (mtpt) cc_final: 0.5320 (mptm)
REVERT: D  113 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7467 (mm-30)
REVERT: D  205 LYS cc_start: 0.8153 (tttt) cc_final: 0.7791 (tttp)
REVERT: D  234 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6860 (mtpp)
REVERT: D  259 MET cc_start: 0.7767 (mtm) cc_final: 0.7545 (mtm)
REVERT: D  311 LYS cc_start: 0.7409 (mmpt) cc_final: 0.6796 (mmpt)
REVERT: D  329 LYS cc_start: 0.6611 (mtpt) cc_final: 0.5372 (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: 1.2216
  time to fit residues: 336.0514
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  : 1.530 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0970
   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:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.156295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.119177 restraints weight = 14151.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.86
r_work: 0.3204 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13472  Z= 0.190
  Angle     :  0.582   4.895  18328  Z= 0.306
  Chirality :  0.045   0.149   1948
  Planarity :  0.005   0.042   2344
  Dihedral  :  4.502  16.154   1780
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 11.48 %
    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: -1.11 (0.21), residues: 1632
  helix: -0.16 (0.18), residues: 720
  sheet: -1.51 (0.28), residues: 348
  loop : -0.66 (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   0.011   0.001   PHE B 310 
 TYR   0.022   0.002   TYR C 264 
 ARG   0.004   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  728)
  hydrogen bonds       : angle       5.93268 ( 2076)
  covalent geometry    : bond        0.00465 (13472)
  covalent geometry    : angle       0.58235 (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
  244 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 196
  time to evaluate  : 1.501 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7813 (tt0) cc_final: 0.7524 (mm-30)
REVERT: A  205 LYS cc_start: 0.8195 (tttt) cc_final: 0.7899 (tttm)
REVERT: A  230 GLU cc_start: 0.7048 (tt0) cc_final: 0.6443 (tm-30)
REVERT: A  234 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6524 (mmpt)
REVERT: A  259 MET cc_start: 0.7782 (mtm) cc_final: 0.7398 (mtp)
REVERT: A  311 LYS cc_start: 0.7401 (mmpt) cc_final: 0.6722 (mmtt)
REVERT: A  329 LYS cc_start: 0.6623 (mtpt) cc_final: 0.5349 (mptm)
REVERT: A  359 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7423 (pm20)
REVERT: B  113 GLU cc_start: 0.7824 (tt0) cc_final: 0.7506 (mm-30)
REVERT: B  205 LYS cc_start: 0.8191 (tttt) cc_final: 0.7897 (tttm)
REVERT: B  234 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6788 (mtpp)
REVERT: B  259 MET cc_start: 0.7773 (mtm) cc_final: 0.7377 (mtp)
REVERT: B  311 LYS cc_start: 0.7390 (mmpt) cc_final: 0.6711 (mmtt)
REVERT: B  329 LYS cc_start: 0.6723 (mtpt) cc_final: 0.5445 (mptm)
REVERT: B  359 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7396 (pm20)
REVERT: C  113 GLU cc_start: 0.7817 (tt0) cc_final: 0.7490 (mm-30)
REVERT: C  205 LYS cc_start: 0.8186 (tttt) cc_final: 0.7887 (tttm)
REVERT: C  230 GLU cc_start: 0.7044 (tt0) cc_final: 0.6444 (tm-30)
REVERT: C  234 LYS cc_start: 0.6876 (mmtt) cc_final: 0.6494 (mmpt)
REVERT: C  259 MET cc_start: 0.7792 (mtm) cc_final: 0.7582 (mtm)
REVERT: C  311 LYS cc_start: 0.7399 (mmpt) cc_final: 0.6719 (mmtt)
REVERT: C  329 LYS cc_start: 0.6601 (mtpt) cc_final: 0.5352 (mptm)
REVERT: C  359 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7413 (pm20)
REVERT: C  423 TYR cc_start: 0.8602 (m-80) cc_final: 0.8402 (m-80)
REVERT: D  113 GLU cc_start: 0.7815 (tt0) cc_final: 0.7524 (mm-30)
REVERT: D  205 LYS cc_start: 0.8202 (tttt) cc_final: 0.7903 (tttm)
REVERT: D  230 GLU cc_start: 0.7047 (tt0) cc_final: 0.6440 (tm-30)
REVERT: D  234 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6528 (mmpt)
REVERT: D  259 MET cc_start: 0.7769 (mtm) cc_final: 0.7383 (mtp)
REVERT: D  311 LYS cc_start: 0.7406 (mmpt) cc_final: 0.6727 (mmtt)
REVERT: D  329 LYS cc_start: 0.6619 (mtpt) cc_final: 0.5363 (mptm)
REVERT: D  359 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7379 (pm20)
  outliers start: 48
  outliers final: 27
  residues processed: 229
  average time/residue: 1.2579
  time to fit residues: 313.9098
Evaluate side-chains
  202 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
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   92 ILE
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  359 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  318 ASP
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   92 ILE
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  318 ASP
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:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 142 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.159027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.122351 restraints weight = 14159.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.92
r_work: 0.3262 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2525

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= 0.129
  Angle     :  0.532   4.838  18328  Z= 0.279
  Chirality :  0.043   0.141   1948
  Planarity :  0.005   0.042   2344
  Dihedral  :  4.339  16.431   1780
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.46 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.83 (0.21), residues: 1632
  helix:  0.11 (0.18), residues: 720
  sheet: -1.50 (0.28), residues: 348
  loop : -0.47 (0.27), residues: 564

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  728)
  hydrogen bonds       : angle       5.75670 ( 2076)
  covalent geometry    : bond        0.00307 (13472)
  covalent geometry    : angle       0.53191 (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
  261 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 212
  time to evaluate  : 1.570 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7768 (tt0) cc_final: 0.7407 (mm-30)
REVERT: A  121 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8275 (pt)
REVERT: A  205 LYS cc_start: 0.8216 (tttt) cc_final: 0.7849 (tttp)
REVERT: A  230 GLU cc_start: 0.6972 (tt0) cc_final: 0.6421 (tm-30)
REVERT: A  234 LYS cc_start: 0.6639 (mmtt) cc_final: 0.6085 (mmpt)
REVERT: A  259 MET cc_start: 0.7803 (mtm) cc_final: 0.7446 (mtp)
REVERT: A  274 LYS cc_start: 0.8077 (mttt) cc_final: 0.7779 (mttp)
REVERT: A  311 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6623 (mmtt)
REVERT: A  329 LYS cc_start: 0.6637 (mtpt) cc_final: 0.5377 (mptm)
REVERT: A  359 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7432 (pm20)
REVERT: B  113 GLU cc_start: 0.7746 (tt0) cc_final: 0.7454 (mm-30)
REVERT: B  205 LYS cc_start: 0.8224 (tttt) cc_final: 0.7845 (tttp)
REVERT: B  230 GLU cc_start: 0.7010 (tt0) cc_final: 0.6428 (tm-30)
REVERT: B  234 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6617 (mmpt)
REVERT: B  259 MET cc_start: 0.7796 (mtm) cc_final: 0.7398 (mtp)
REVERT: B  274 LYS cc_start: 0.8053 (mttt) cc_final: 0.7722 (mttp)
REVERT: B  311 LYS cc_start: 0.7304 (mmpt) cc_final: 0.6627 (mmtt)
REVERT: B  329 LYS cc_start: 0.6670 (mtpt) cc_final: 0.5383 (mptm)
REVERT: B  359 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7420 (pm20)
REVERT: C  113 GLU cc_start: 0.7765 (tt0) cc_final: 0.7404 (mm-30)
REVERT: C  121 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8264 (pt)
REVERT: C  205 LYS cc_start: 0.8217 (tttt) cc_final: 0.7852 (tttp)
REVERT: C  230 GLU cc_start: 0.6986 (tt0) cc_final: 0.6450 (tm-30)
REVERT: C  234 LYS cc_start: 0.6657 (mmtt) cc_final: 0.6110 (mmpt)
REVERT: C  259 MET cc_start: 0.7799 (mtm) cc_final: 0.7430 (mtp)
REVERT: C  274 LYS cc_start: 0.8068 (mttt) cc_final: 0.7770 (mttp)
REVERT: C  311 LYS cc_start: 0.7301 (mmpt) cc_final: 0.6624 (mmtt)
REVERT: C  329 LYS cc_start: 0.6617 (mtpt) cc_final: 0.5362 (mptm)
REVERT: C  354 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8122 (m-10)
REVERT: C  423 TYR cc_start: 0.8504 (m-80) cc_final: 0.8117 (m-80)
REVERT: D  113 GLU cc_start: 0.7780 (tt0) cc_final: 0.7410 (mm-30)
REVERT: D  121 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (pt)
REVERT: D  205 LYS cc_start: 0.8220 (tttt) cc_final: 0.7853 (tttp)
REVERT: D  230 GLU cc_start: 0.6962 (tt0) cc_final: 0.6418 (tm-30)
REVERT: D  234 LYS cc_start: 0.6636 (mmtt) cc_final: 0.6081 (mmpt)
REVERT: D  259 MET cc_start: 0.7784 (mtm) cc_final: 0.7425 (mtp)
REVERT: D  274 LYS cc_start: 0.8077 (mttt) cc_final: 0.7774 (mttp)
REVERT: D  311 LYS cc_start: 0.7296 (mmpt) cc_final: 0.6607 (mmtt)
REVERT: D  329 LYS cc_start: 0.6598 (mtpt) cc_final: 0.5349 (mptm)
REVERT: D  359 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7391 (pm20)
  outliers start: 49
  outliers final: 22
  residues processed: 245
  average time/residue: 1.2146
  time to fit residues: 325.1503
Evaluate side-chains
  209 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 180
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
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  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  106 SER
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  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  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  411 LEU
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  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:    0.0980
   chunk 92 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 158 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 123 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.159979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.123168 restraints weight = 14139.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.93
r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13472  Z= 0.118
  Angle     :  0.518   4.953  18328  Z= 0.272
  Chirality :  0.042   0.145   1948
  Planarity :  0.004   0.039   2344
  Dihedral  :  4.214  16.536   1780
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.38 %
    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: -0.36 (0.21), residues: 1632
  helix:  0.49 (0.19), residues: 692
  sheet: -1.48 (0.28), residues: 344
  loop : -0.06 (0.28), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  27 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.010   0.001   PHE B 310 
 TYR   0.020   0.001   TYR B 264 
 ARG   0.006   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03232 (  728)
  hydrogen bonds       : angle       5.65669 ( 2076)
  covalent geometry    : bond        0.00280 (13472)
  covalent geometry    : angle       0.51758 (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
  248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 200
  time to evaluate  : 1.498 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7580 (tt0) cc_final: 0.7218 (mm-30)
REVERT: A  121 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8329 (pt)
REVERT: A  205 LYS cc_start: 0.8215 (tttt) cc_final: 0.7874 (tttp)
REVERT: A  234 LYS cc_start: 0.6754 (mmtt) cc_final: 0.6239 (pttt)
REVERT: A  259 MET cc_start: 0.7812 (mtm) cc_final: 0.7470 (mtp)
REVERT: A  274 LYS cc_start: 0.8054 (mttt) cc_final: 0.7730 (mttp)
REVERT: A  311 LYS cc_start: 0.7290 (mmpt) cc_final: 0.6599 (mmtt)
REVERT: A  329 LYS cc_start: 0.6662 (mtpt) cc_final: 0.5433 (mptm)
REVERT: A  423 TYR cc_start: 0.8437 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  113 GLU cc_start: 0.7575 (tt0) cc_final: 0.7224 (mm-30)
REVERT: B  121 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (pt)
REVERT: B  205 LYS cc_start: 0.8214 (tttt) cc_final: 0.7872 (tttp)
REVERT: B  230 GLU cc_start: 0.6973 (tt0) cc_final: 0.6436 (tm-30)
REVERT: B  234 LYS cc_start: 0.6818 (mmtt) cc_final: 0.6419 (mmpt)
REVERT: B  259 MET cc_start: 0.7809 (mtm) cc_final: 0.7419 (mtp)
REVERT: B  274 LYS cc_start: 0.8024 (mttt) cc_final: 0.7703 (mttp)
REVERT: B  311 LYS cc_start: 0.7286 (mmpt) cc_final: 0.6596 (mmtt)
REVERT: B  329 LYS cc_start: 0.6750 (mtpt) cc_final: 0.5412 (mptm)
REVERT: C  113 GLU cc_start: 0.7600 (tt0) cc_final: 0.7229 (mm-30)
REVERT: C  121 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (pt)
REVERT: C  205 LYS cc_start: 0.8218 (tttt) cc_final: 0.7875 (tttp)
REVERT: C  234 LYS cc_start: 0.6775 (mmtt) cc_final: 0.6264 (pttt)
REVERT: C  259 MET cc_start: 0.7806 (mtm) cc_final: 0.7452 (mtp)
REVERT: C  274 LYS cc_start: 0.7958 (mttt) cc_final: 0.7666 (mttp)
REVERT: C  311 LYS cc_start: 0.7282 (mmpt) cc_final: 0.6592 (mmtt)
REVERT: C  329 LYS cc_start: 0.6658 (mtpt) cc_final: 0.5431 (mptm)
REVERT: C  423 TYR cc_start: 0.8478 (m-80) cc_final: 0.8043 (m-80)
REVERT: D  113 GLU cc_start: 0.7609 (tt0) cc_final: 0.7236 (mm-30)
REVERT: D  121 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8342 (pt)
REVERT: D  205 LYS cc_start: 0.8213 (tttt) cc_final: 0.7873 (tttp)
REVERT: D  234 LYS cc_start: 0.6754 (mmtt) cc_final: 0.6199 (mtpp)
REVERT: D  259 MET cc_start: 0.7805 (mtm) cc_final: 0.7461 (mtp)
REVERT: D  274 LYS cc_start: 0.8035 (mttt) cc_final: 0.7718 (mttp)
REVERT: D  311 LYS cc_start: 0.7294 (mmpt) cc_final: 0.6603 (mmtt)
REVERT: D  329 LYS cc_start: 0.6639 (mtpt) cc_final: 0.5420 (mptm)
REVERT: D  423 TYR cc_start: 0.8444 (m-80) cc_final: 0.8109 (m-80)
  outliers start: 48
  outliers final: 13
  residues processed: 228
  average time/residue: 1.2686
  time to fit residues: 315.3698
Evaluate side-chains
  202 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.592 
-------------------------------------------------------------------------------
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  342 MET
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  354 TYR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain C residue  342 MET
Chi-restraints excluded: chain C residue  354 TYR
Chi-restraints excluded: chain C residue  411 LEU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  121 ILE
Chi-restraints excluded: chain D residue  342 MET
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:    0.7980
   chunk 138 optimal weight:    0.7980
   chunk 123 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 151 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.158991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.122539 restraints weight = 14471.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.93
r_work: 0.3251 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2779

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= 0.137
  Angle     :  0.538   4.852  18328  Z= 0.282
  Chirality :  0.042   0.139   1948
  Planarity :  0.005   0.042   2344
  Dihedral  :  4.225  16.525   1780
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.96 %
    Favored  : 83.73 %
  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: -0.32 (0.21), residues: 1632
  helix:  0.55 (0.19), residues: 692
  sheet: -1.46 (0.28), residues: 344
  loop : -0.08 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  27 
 HIS   0.004   0.001   HIS B  69 
 PHE   0.010   0.001   PHE C 226 
 TYR   0.020   0.001   TYR D 264 
 ARG   0.008   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03275 (  728)
  hydrogen bonds       : angle       5.63927 ( 2076)
  covalent geometry    : bond        0.00327 (13472)
  covalent geometry    : angle       0.53765 (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
  248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 201
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7176 (mm-30)
REVERT: A  121 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8329 (pt)
REVERT: A  205 LYS cc_start: 0.8207 (tttt) cc_final: 0.7847 (tttp)
REVERT: A  230 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6806 (tm-30)
REVERT: A  259 MET cc_start: 0.7772 (mtm) cc_final: 0.7433 (mtp)
REVERT: A  274 LYS cc_start: 0.8052 (mttt) cc_final: 0.7727 (mttp)
REVERT: A  311 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6625 (mmtt)
REVERT: A  329 LYS cc_start: 0.6708 (mtpt) cc_final: 0.5335 (mptm)
REVERT: A  423 TYR cc_start: 0.8490 (m-80) cc_final: 0.8157 (m-80)
REVERT: B  113 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7168 (mm-30)
REVERT: B  121 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8279 (pt)
REVERT: B  205 LYS cc_start: 0.8191 (tttt) cc_final: 0.7835 (tttp)
REVERT: B  234 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6291 (mtpp)
REVERT: B  259 MET cc_start: 0.7786 (mtm) cc_final: 0.7417 (mtp)
REVERT: B  274 LYS cc_start: 0.8069 (mttt) cc_final: 0.7743 (mttp)
REVERT: B  311 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6627 (mmtt)
REVERT: B  329 LYS cc_start: 0.6739 (mtpt) cc_final: 0.5374 (mptm)
REVERT: C  113 GLU cc_start: 0.7615 (tt0) cc_final: 0.7180 (mm-30)
REVERT: C  121 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (pt)
REVERT: C  205 LYS cc_start: 0.8202 (tttt) cc_final: 0.7844 (tttp)
REVERT: C  230 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: C  259 MET cc_start: 0.7794 (mtm) cc_final: 0.7448 (mtp)
REVERT: C  274 LYS cc_start: 0.7990 (mttt) cc_final: 0.7697 (mttp)
REVERT: C  311 LYS cc_start: 0.7326 (mmpt) cc_final: 0.6623 (mmtt)
REVERT: C  329 LYS cc_start: 0.6702 (mtpt) cc_final: 0.5354 (mptm)
REVERT: C  423 TYR cc_start: 0.8490 (m-80) cc_final: 0.8044 (m-80)
REVERT: D  113 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7178 (mm-30)
REVERT: D  121 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (pt)
REVERT: D  205 LYS cc_start: 0.8214 (tttt) cc_final: 0.7851 (tttp)
REVERT: D  230 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6828 (tm-30)
REVERT: D  259 MET cc_start: 0.7776 (mtm) cc_final: 0.7437 (mtp)
REVERT: D  274 LYS cc_start: 0.8057 (mttt) cc_final: 0.7733 (mttp)
REVERT: D  311 LYS cc_start: 0.7340 (mmpt) cc_final: 0.6635 (mmtt)
REVERT: D  329 LYS cc_start: 0.6714 (mtpt) cc_final: 0.5365 (mptm)
REVERT: D  423 TYR cc_start: 0.8485 (m-80) cc_final: 0.8156 (m-80)
  outliers start: 47
  outliers final: 24
  residues processed: 229
  average time/residue: 1.2643
  time to fit residues: 315.1258
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  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  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  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  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  121 ILE
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  318 ASP
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 162 optimal weight:    0.5980
   chunk 70 optimal weight:    8.9990
   chunk 123 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 156 optimal weight:    7.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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
D 255 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.120757 restraints weight = 14347.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.86
r_work: 0.3226 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13472  Z= 0.176
  Angle     :  0.566   5.474  18328  Z= 0.296
  Chirality :  0.044   0.150   1948
  Planarity :  0.005   0.048   2344
  Dihedral  :  4.340  16.730   1780
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 13.73 %
    Favored  : 82.25 %
  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: -0.39 (0.21), residues: 1632
  helix:  0.52 (0.19), residues: 692
  sheet: -1.56 (0.27), residues: 348
  loop : -0.08 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  27 
 HIS   0.005   0.001   HIS D  69 
 PHE   0.010   0.001   PHE B 226 
 TYR   0.020   0.002   TYR B 264 
 ARG   0.010   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03497 (  728)
  hydrogen bonds       : angle       5.72968 ( 2076)
  covalent geometry    : bond        0.00430 (13472)
  covalent geometry    : angle       0.56636 (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
  265 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 208
  time to evaluate  : 1.418 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7694 (tt0) cc_final: 0.7265 (mm-30)
REVERT: A  121 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8258 (pt)
REVERT: A  205 LYS cc_start: 0.8074 (tttt) cc_final: 0.7756 (tttp)
REVERT: A  230 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6533 (tm-30)
REVERT: A  234 LYS cc_start: 0.6673 (mmpt) cc_final: 0.6091 (mmpt)
REVERT: A  259 MET cc_start: 0.7710 (mtm) cc_final: 0.7350 (mtp)
REVERT: A  274 LYS cc_start: 0.8109 (mttt) cc_final: 0.7805 (mttp)
REVERT: A  311 LYS cc_start: 0.7350 (mmpt) cc_final: 0.6630 (mmtt)
REVERT: A  329 LYS cc_start: 0.6748 (mtpt) cc_final: 0.5397 (mptm)
REVERT: A  423 TYR cc_start: 0.8524 (m-80) cc_final: 0.8220 (m-80)
REVERT: B  113 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7260 (mm-30)
REVERT: B  205 LYS cc_start: 0.8086 (tttt) cc_final: 0.7760 (tttp)
REVERT: B  217 MET cc_start: 0.8247 (mtm) cc_final: 0.7938 (mtt)
REVERT: B  230 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6816 (tm-30)
REVERT: B  259 MET cc_start: 0.7744 (mtm) cc_final: 0.7524 (mtm)
REVERT: B  274 LYS cc_start: 0.8091 (mttt) cc_final: 0.7784 (mttp)
REVERT: B  311 LYS cc_start: 0.7341 (mmpt) cc_final: 0.6623 (mmtt)
REVERT: B  329 LYS cc_start: 0.6803 (mtpt) cc_final: 0.5479 (mptm)
REVERT: C  113 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7272 (mm-30)
REVERT: C  121 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8246 (pt)
REVERT: C  205 LYS cc_start: 0.8068 (tttt) cc_final: 0.7742 (tttp)
REVERT: C  230 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6947 (tm-30)
REVERT: C  259 MET cc_start: 0.7778 (mtm) cc_final: 0.7299 (mtp)
REVERT: C  274 LYS cc_start: 0.8091 (mttt) cc_final: 0.7789 (mttp)
REVERT: C  311 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6616 (mmtt)
REVERT: C  329 LYS cc_start: 0.6751 (mtpt) cc_final: 0.5413 (mptm)
REVERT: C  423 TYR cc_start: 0.8561 (m-80) cc_final: 0.8239 (m-80)
REVERT: D  113 GLU cc_start: 0.7696 (tt0) cc_final: 0.7254 (mm-30)
REVERT: D  121 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8272 (pt)
REVERT: D  205 LYS cc_start: 0.8087 (tttt) cc_final: 0.7773 (tttp)
REVERT: D  230 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6564 (tm-30)
REVERT: D  234 LYS cc_start: 0.6690 (mmpt) cc_final: 0.6111 (mmpt)
REVERT: D  259 MET cc_start: 0.7718 (mtm) cc_final: 0.7367 (mtp)
REVERT: D  274 LYS cc_start: 0.8120 (mttt) cc_final: 0.7817 (mttp)
REVERT: D  311 LYS cc_start: 0.7331 (mmpt) cc_final: 0.6610 (mmtt)
REVERT: D  329 LYS cc_start: 0.6726 (mtpt) cc_final: 0.5406 (mptm)
REVERT: D  423 TYR cc_start: 0.8515 (m-80) cc_final: 0.8216 (m-80)
  outliers start: 57
  outliers final: 33
  residues processed: 244
  average time/residue: 1.2110
  time to fit residues: 322.8465
Evaluate side-chains
  225 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 187
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
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   92 ILE
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  121 ILE
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  354 TYR
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  325 LEU
Chi-restraints excluded: chain B residue  354 TYR
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  121 ILE
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  354 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9980
   chunk 146 optimal weight:   10.0000
   chunk 38 optimal weight:    0.2980
   chunk 93 optimal weight:    1.9990
   chunk 144 optimal weight:    9.9990
   chunk 130 optimal weight:    0.1980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 255 HIS
C 255 HIS
D 136 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 = 0.3830 r_free = 0.3830 target = 0.162349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.125893 restraints weight = 14363.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.02
r_work: 0.3278 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13472  Z= 0.107
  Angle     :  0.515   4.937  18328  Z= 0.271
  Chirality :  0.042   0.138   1948
  Planarity :  0.005   0.041   2344
  Dihedral  :  4.157  16.395   1780
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.30 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.17 (0.21), residues: 1632
  helix:  0.72 (0.19), residues: 692
  sheet: -1.43 (0.27), residues: 344
  loop : -0.03 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  27 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.009   0.001   PHE C 226 
 TYR   0.018   0.001   TYR C 264 
 ARG   0.008   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03060 (  728)
  hydrogen bonds       : angle       5.55992 ( 2076)
  covalent geometry    : bond        0.00249 (13472)
  covalent geometry    : angle       0.51480 (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
  265 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 221
  time to evaluate  : 1.545 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7139 (mm-30)
REVERT: A  205 LYS cc_start: 0.8216 (tttt) cc_final: 0.7886 (tttp)
REVERT: A  217 MET cc_start: 0.8358 (mtm) cc_final: 0.8059 (mtt)
REVERT: A  230 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6751 (tm-30)
REVERT: A  234 LYS cc_start: 0.6821 (mmpt) cc_final: 0.6212 (mmpt)
REVERT: A  259 MET cc_start: 0.7821 (mtm) cc_final: 0.7507 (mtp)
REVERT: A  274 LYS cc_start: 0.8037 (mttt) cc_final: 0.7708 (mttp)
REVERT: A  311 LYS cc_start: 0.7290 (mmpt) cc_final: 0.6529 (mmtt)
REVERT: A  329 LYS cc_start: 0.6714 (mtpt) cc_final: 0.5582 (mptt)
REVERT: A  423 TYR cc_start: 0.8441 (m-80) cc_final: 0.8100 (m-80)
REVERT: B  113 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7133 (mm-30)
REVERT: B  121 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8334 (pt)
REVERT: B  205 LYS cc_start: 0.8210 (tttt) cc_final: 0.7886 (tttp)
REVERT: B  230 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6752 (tm-30)
REVERT: B  234 LYS cc_start: 0.6719 (mmpt) cc_final: 0.6244 (mmpt)
REVERT: B  259 MET cc_start: 0.7807 (mtm) cc_final: 0.7476 (mtp)
REVERT: B  274 LYS cc_start: 0.7999 (mttt) cc_final: 0.7688 (mttp)
REVERT: B  311 LYS cc_start: 0.7247 (mmpt) cc_final: 0.6478 (mmtt)
REVERT: B  329 LYS cc_start: 0.6756 (mtpt) cc_final: 0.5636 (mptt)
REVERT: C  113 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7149 (mm-30)
REVERT: C  205 LYS cc_start: 0.8216 (tttt) cc_final: 0.7884 (tttp)
REVERT: C  217 MET cc_start: 0.8366 (mtm) cc_final: 0.8064 (mtt)
REVERT: C  259 MET cc_start: 0.7795 (mtm) cc_final: 0.7493 (mtp)
REVERT: C  274 LYS cc_start: 0.8042 (mttt) cc_final: 0.7711 (mttp)
REVERT: C  311 LYS cc_start: 0.7291 (mmpt) cc_final: 0.6528 (mmtt)
REVERT: C  329 LYS cc_start: 0.6726 (mtpt) cc_final: 0.5598 (mptt)
REVERT: C  423 TYR cc_start: 0.8488 (m-80) cc_final: 0.8037 (m-80)
REVERT: D  113 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7152 (mm-30)
REVERT: D  205 LYS cc_start: 0.8213 (tttt) cc_final: 0.7887 (tttp)
REVERT: D  217 MET cc_start: 0.8363 (mtm) cc_final: 0.8059 (mtt)
REVERT: D  230 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6669 (tm-30)
REVERT: D  234 LYS cc_start: 0.6783 (mmpt) cc_final: 0.6165 (mmpt)
REVERT: D  259 MET cc_start: 0.7796 (mtm) cc_final: 0.7480 (mtp)
REVERT: D  274 LYS cc_start: 0.8064 (mttt) cc_final: 0.7735 (mttp)
REVERT: D  311 LYS cc_start: 0.7289 (mmpt) cc_final: 0.6519 (mmtt)
REVERT: D  329 LYS cc_start: 0.6711 (mtpt) cc_final: 0.5585 (mptt)
REVERT: D  423 TYR cc_start: 0.8445 (m-80) cc_final: 0.8113 (m-80)
  outliers start: 44
  outliers final: 18
  residues processed: 242
  average time/residue: 1.3004
  time to fit residues: 342.7238
Evaluate side-chains
  221 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
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  325 LEU
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  325 LEU
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  113 GLU
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  113 GLU
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:    2.9990
   chunk 104 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 133 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    8.9990
   chunk 153 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 143 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 146 optimal weight:   10.0000
   overall best weight:    2.3988

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.155123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.119036 restraints weight = 14349.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.82
r_work: 0.3189 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13472  Z= 0.229
  Angle     :  0.611   6.873  18328  Z= 0.319
  Chirality :  0.046   0.187   1948
  Planarity :  0.005   0.058   2344
  Dihedral  :  4.483  16.800   1780
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.00 %
    Favored  : 82.04 %
  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: -0.47 (0.21), residues: 1632
  helix:  0.50 (0.19), residues: 692
  sheet: -1.59 (0.27), residues: 352
  loop : -0.19 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 317 
 HIS   0.006   0.001   HIS C  69 
 PHE   0.010   0.002   PHE C 226 
 TYR   0.021   0.002   TYR D 264 
 ARG   0.011   0.001   ARG D 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  728)
  hydrogen bonds       : angle       5.78159 ( 2076)
  covalent geometry    : bond        0.00566 (13472)
  covalent geometry    : angle       0.61131 (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
  244 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 202
  time to evaluate  : 1.526 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7719 (tt0) cc_final: 0.7245 (mm-30)
REVERT: A  217 MET cc_start: 0.8370 (mtm) cc_final: 0.8061 (mtt)
REVERT: A  230 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7066 (tm-30)
REVERT: A  234 LYS cc_start: 0.6771 (mmpt) cc_final: 0.6354 (mtpp)
REVERT: A  259 MET cc_start: 0.7718 (mtm) cc_final: 0.7350 (mtp)
REVERT: A  274 LYS cc_start: 0.8245 (mttt) cc_final: 0.7912 (mttp)
REVERT: A  311 LYS cc_start: 0.7221 (mmpt) cc_final: 0.6487 (mmtt)
REVERT: A  329 LYS cc_start: 0.6769 (mtpt) cc_final: 0.5466 (mptm)
REVERT: B  113 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7229 (mm-30)
REVERT: B  230 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6792 (tm-30)
REVERT: B  234 LYS cc_start: 0.6703 (mmpt) cc_final: 0.6184 (mmpt)
REVERT: B  259 MET cc_start: 0.7759 (mtm) cc_final: 0.7546 (mtm)
REVERT: B  274 LYS cc_start: 0.8209 (mttt) cc_final: 0.7880 (mttp)
REVERT: B  311 LYS cc_start: 0.7183 (mmpt) cc_final: 0.6454 (mmtt)
REVERT: B  324 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6957 (pp20)
REVERT: B  329 LYS cc_start: 0.6782 (mtpt) cc_final: 0.5635 (mptt)
REVERT: C  113 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7228 (mm-30)
REVERT: C  217 MET cc_start: 0.8373 (mtm) cc_final: 0.8063 (mtt)
REVERT: C  259 MET cc_start: 0.7753 (mtm) cc_final: 0.7497 (mtm)
REVERT: C  274 LYS cc_start: 0.8199 (mttt) cc_final: 0.7869 (mttp)
REVERT: C  311 LYS cc_start: 0.7222 (mmpt) cc_final: 0.6492 (mmtt)
REVERT: C  324 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6977 (pp20)
REVERT: C  329 LYS cc_start: 0.6735 (mtpt) cc_final: 0.5448 (mptm)
REVERT: C  423 TYR cc_start: 0.8597 (m-80) cc_final: 0.8340 (m-80)
REVERT: D  113 GLU cc_start: 0.7717 (tt0) cc_final: 0.7232 (mm-30)
REVERT: D  217 MET cc_start: 0.8352 (mtm) cc_final: 0.8041 (mtt)
REVERT: D  230 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7057 (tm-30)
REVERT: D  234 LYS cc_start: 0.6778 (mmpt) cc_final: 0.6356 (mtpp)
REVERT: D  259 MET cc_start: 0.7726 (mtm) cc_final: 0.7353 (mtp)
REVERT: D  274 LYS cc_start: 0.8240 (mttt) cc_final: 0.7901 (mttp)
REVERT: D  311 LYS cc_start: 0.7244 (mmpt) cc_final: 0.6536 (mmtt)
REVERT: D  329 LYS cc_start: 0.6751 (mtpt) cc_final: 0.5448 (mptm)
  outliers start: 42
  outliers final: 27
  residues processed: 224
  average time/residue: 1.2046
  time to fit residues: 296.1982
Evaluate side-chains
  217 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 186
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
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  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  324 GLU
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   92 ILE
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  318 ASP
Chi-restraints excluded: chain C residue  320 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  325 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  318 ASP
Chi-restraints excluded: chain D residue  324 GLU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  411 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 126 optimal weight:    0.5980
   chunk 127 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9980
   chunk 118 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.160232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.124329 restraints weight = 14238.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.88
r_work: 0.3275 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3018

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= 0.120
  Angle     :  0.535   6.747  18328  Z= 0.282
  Chirality :  0.042   0.143   1948
  Planarity :  0.005   0.047   2344
  Dihedral  :  4.259  17.092   1780
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.92 %
    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: -0.23 (0.21), residues: 1632
  helix:  0.69 (0.19), residues: 692
  sheet: -1.44 (0.27), residues: 344
  loop : -0.09 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 408 
 HIS   0.003   0.001   HIS B 385 
 PHE   0.010   0.001   PHE C 226 
 TYR   0.019   0.001   TYR C 264 
 ARG   0.011   0.001   ARG B 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03168 (  728)
  hydrogen bonds       : angle       5.58865 ( 2076)
  covalent geometry    : bond        0.00284 (13472)
  covalent geometry    : angle       0.53517 (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
  233 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 1.553 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.7512 (tt0) cc_final: 0.7097 (mm-30)
REVERT: A  205 LYS cc_start: 0.8175 (tttt) cc_final: 0.7797 (tttp)
REVERT: A  217 MET cc_start: 0.8348 (mtm) cc_final: 0.8023 (mtt)
REVERT: A  234 LYS cc_start: 0.6725 (mmpt) cc_final: 0.6331 (mtpp)
REVERT: A  259 MET cc_start: 0.7762 (mtm) cc_final: 0.7537 (mtm)
REVERT: A  274 LYS cc_start: 0.8023 (mttt) cc_final: 0.7706 (mttp)
REVERT: A  311 LYS cc_start: 0.7211 (mmpt) cc_final: 0.6508 (mmtt)
REVERT: A  329 LYS cc_start: 0.6733 (mtpt) cc_final: 0.5634 (mptt)
REVERT: A  423 TYR cc_start: 0.8471 (m-80) cc_final: 0.8000 (m-80)
REVERT: B  113 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7087 (mm-30)
REVERT: B  121 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8292 (pt)
REVERT: B  205 LYS cc_start: 0.8165 (tttt) cc_final: 0.7798 (tttp)
REVERT: B  230 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: B  234 LYS cc_start: 0.6731 (mmpt) cc_final: 0.6151 (mmpt)
REVERT: B  259 MET cc_start: 0.7765 (mtm) cc_final: 0.7442 (mtp)
REVERT: B  274 LYS cc_start: 0.8058 (mttt) cc_final: 0.7738 (mttp)
REVERT: B  311 LYS cc_start: 0.7196 (mmpt) cc_final: 0.6428 (mmtt)
REVERT: B  329 LYS cc_start: 0.6802 (mtpt) cc_final: 0.5625 (mptt)
REVERT: C  113 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7094 (mm-30)
REVERT: C  205 LYS cc_start: 0.8183 (tttt) cc_final: 0.7808 (tttp)
REVERT: C  217 MET cc_start: 0.8352 (mtm) cc_final: 0.8028 (mtt)
REVERT: C  259 MET cc_start: 0.7760 (mtm) cc_final: 0.7543 (mtm)
REVERT: C  274 LYS cc_start: 0.8097 (mttt) cc_final: 0.7737 (mttp)
REVERT: C  311 LYS cc_start: 0.7248 (mmpt) cc_final: 0.6535 (mmtt)
REVERT: C  329 LYS cc_start: 0.6737 (mtpt) cc_final: 0.5645 (mptt)
REVERT: C  423 TYR cc_start: 0.8511 (m-80) cc_final: 0.8040 (m-80)
REVERT: D  113 GLU cc_start: 0.7522 (tt0) cc_final: 0.7108 (mm-30)
REVERT: D  205 LYS cc_start: 0.8179 (tttt) cc_final: 0.7807 (tttp)
REVERT: D  217 MET cc_start: 0.8334 (mtm) cc_final: 0.8011 (mtt)
REVERT: D  221 MET cc_start: 0.7614 (mmt) cc_final: 0.7285 (mmt)
REVERT: D  234 LYS cc_start: 0.6761 (mmpt) cc_final: 0.6361 (mtpp)
REVERT: D  259 MET cc_start: 0.7752 (mtm) cc_final: 0.7526 (mtm)
REVERT: D  274 LYS cc_start: 0.8031 (mttt) cc_final: 0.7710 (mttp)
REVERT: D  311 LYS cc_start: 0.7253 (mmpt) cc_final: 0.6549 (mmtt)
REVERT: D  329 LYS cc_start: 0.6729 (mtpt) cc_final: 0.5506 (mptm)
REVERT: D  423 TYR cc_start: 0.8376 (m-80) cc_final: 0.8045 (m-80)
  outliers start: 28
  outliers final: 17
  residues processed: 215
  average time/residue: 1.2529
  time to fit residues: 293.6879
Evaluate side-chains
  210 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
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  325 LEU
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  320 ILE
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  113 GLU
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 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  411 LEU
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:    6.9990
   chunk 104 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.1784

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.158379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.122331 restraints weight = 14305.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.91
r_work: 0.3246 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13472  Z= 0.147
  Angle     :  0.562   7.511  18328  Z= 0.294
  Chirality :  0.043   0.160   1948
  Planarity :  0.005   0.049   2344
  Dihedral  :  4.294  17.115   1780
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.85 %
    Favored  : 81.90 %
  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: -0.19 (0.21), residues: 1632
  helix:  0.70 (0.19), residues: 692
  sheet: -1.37 (0.27), residues: 344
  loop : -0.08 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 317 
 HIS   0.004   0.001   HIS B 385 
 PHE   0.010   0.001   PHE C 226 
 TYR   0.023   0.002   TYR A 354 
 ARG   0.010   0.001   ARG C 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  728)
  hydrogen bonds       : angle       5.62346 ( 2076)
  covalent geometry    : bond        0.00354 (13472)
  covalent geometry    : angle       0.56163 (18328)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9504.35 seconds
wall clock time: 164 minutes 23.80 seconds (9863.80 seconds total)