Starting phenix.real_space_refine
on Thu Mar 13 21:56:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ba5_44396/03_2025/9ba5_44396.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic.
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      42      5.16       5
     C    5666      2.51       5
     N    1570      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9012
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4436
          Classifications: {'peptide': 573}
          Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535}
    Chain: "B"
      Number of atoms: 4436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4436
          Classifications: {'peptide': 573}
          Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 5.98, per 1000 atoms: 0.66
  Number of scatterers: 9012
  At special positions: 0
  Unit cell: (197.4, 80.85, 99.75, 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      42     16.00
     O    1734      8.00
     N    1570      7.00
     C    5666      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 111 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 261 " - pdb=" SG  CYS A 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 440 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 587 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 111 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 261 " - pdb=" SG  CYS B 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 348 " - pdb=" SG  CYS B 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 440 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 587 " distance=2.02

  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
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A  76 "
      " NAG A 702 " - " ASN A 198 "
      " NAG A 703 " - " ASN A 461 "
      " NAG A 704 " - " ASN A 498 "
      " NAG A 705 " - " ASN A 525 "
      " NAG B 701 " - " ASN B  76 "
      " NAG B 702 " - " ASN B 198 "
      " NAG B 703 " - " ASN B 461 "
      " NAG B 704 " - " ASN B 498 "
      " NAG B 705 " - " ASN B 525 "
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 38 sheets defined
      4.5% alpha, 43.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 4.236A  pdb=" N   ALA A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 202
      removed outlier: 4.226A  pdb=" N   LEU A 202 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.774A  pdb=" N   SER A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.936A  pdb=" N   GLU A 483 " --> pdb=" O   ARG A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 4.124A  pdb=" N   GLY A 582 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
      removed outlier: 4.002A  pdb=" N   ALA B 106 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.537A  pdb=" N   ASP B 201 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LEU B 202 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 198 through 202'
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.845A  pdb=" N   SER B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 3.701A  pdb=" N   GLU B 483 " --> pdb=" O   ARG B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 582
      removed outlier: 4.135A  pdb=" N   GLY B 582 " --> pdb=" O   LEU B 579 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41
      removed outlier: 6.275A  pdb=" N   GLY A  36 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   SER A  66 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG A  62 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48
    Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48
    Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59
    Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 147
      removed outlier: 6.303A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA A 230 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ALA A 145 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   GLU A 232 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 206 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 147
      removed outlier: 6.303A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA A 230 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ALA A 145 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   GLU A 232 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153
    Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252
      removed outlier: 6.142A  pdb=" N   THR A 249 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLN A 324 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260
    Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331
      removed outlier: 6.828A  pdb=" N   ALA A 349 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339
      removed outlier: 6.499A  pdb=" N   THR A 336 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLN A 413 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA A 338 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A 398 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 346
    Processing sheet with id=AB5, first strand: chain 'A' and resid 415 through 418
      removed outlier: 3.656A  pdb=" N   ALA A 445 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ARG A 443 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 427 through 431
    Processing sheet with id=AB7, first strand: chain 'A' and resid 435 through 439
    Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513
      removed outlier: 6.687A  pdb=" N   HIS A 531 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 519
    Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528
    Processing sheet with id=AC2, first strand: chain 'B' and resid 35 through 41
      removed outlier: 6.202A  pdb=" N   GLY B  36 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   SER B  66 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ARG B  62 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 46 through 48
      removed outlier: 3.551A  pdb=" N   THR B  78 " --> pdb=" O   MET B  75 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 46 through 48
    Processing sheet with id=AC5, first strand: chain 'B' and resid 56 through 59
    Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 132
      removed outlier: 3.516A  pdb=" N   PHE B 131 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 143 through 147
      removed outlier: 6.295A  pdb=" N   VAL B 143 " --> pdb=" O   ASN B 228 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   ALA B 230 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   ALA B 145 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   GLU B 232 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   GLU B 147 " --> pdb=" O   GLU B 232 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 153
    Processing sheet with id=AC9, first strand: chain 'B' and resid 165 through 168
    Processing sheet with id=AD1, first strand: chain 'B' and resid 241 through 244
    Processing sheet with id=AD2, first strand: chain 'B' and resid 248 through 251
    Processing sheet with id=AD3, first strand: chain 'B' and resid 328 through 331
      removed outlier: 6.749A  pdb=" N   ALA B 349 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 336 through 339
      removed outlier: 6.573A  pdb=" N   THR B 336 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN B 413 " --> pdb=" O   THR B 336 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA B 338 " --> pdb=" O   GLN B 413 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR B 357 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 344 through 346
    Processing sheet with id=AD6, first strand: chain 'B' and resid 415 through 418
      removed outlier: 3.656A  pdb=" N   ALA B 445 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ARG B 443 " --> pdb=" O   PRO B 417 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 427 through 431
      removed outlier: 6.539A  pdb=" N   ILE B 428 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ARG B 506 " --> pdb=" O   ILE B 428 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ALA B 430 " --> pdb=" O   ARG B 506 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'B' and resid 435 through 439
    Processing sheet with id=AD9, first strand: chain 'B' and resid 510 through 513
      removed outlier: 6.783A  pdb=" N   HIS B 531 " --> pdb=" O   THR B 512 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'B' and resid 518 through 519
      removed outlier: 3.550A  pdb=" N   LEU B 603 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'B' and resid 526 through 528

    316 hydrogen bonds defined for protein.
    723 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: 3.75

  Time building geometry restraints manager: 2.83 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: 2901
        1.34 -     1.46: 2109
        1.46 -     1.58: 4148
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 9218
  Sorted by residual:
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.558 -0.152 2.00e-02 2.50e+03 5.77e+01
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.558 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" C1  NAG B 705 "
       pdb=" O5  NAG B 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.544 -0.138 2.00e-02 2.50e+03 4.74e+01
  bond pdb=" C1  NAG B 701 "
       pdb=" O5  NAG B 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.543 -0.137 2.00e-02 2.50e+03 4.68e+01
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.542 -0.136 2.00e-02 2.50e+03 4.62e+01
  ... (remaining 9213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 12218
        3.60 -     7.21: 295
        7.21 -    10.81: 22
       10.81 -    14.42: 3
       14.42 -    18.02: 2
  Bond angle restraints: 12540
  Sorted by residual:
  angle pdb=" CG1 VAL B  91 "
        pdb=" CB  VAL B  91 "
        pdb=" CG2 VAL B  91 "
      ideal   model   delta    sigma   weight residual
     110.80   99.34   11.46 2.20e+00 2.07e-01 2.71e+01
  angle pdb=" CA  LEU A 376 "
        pdb=" CB  LEU A 376 "
        pdb=" CG  LEU A 376 "
      ideal   model   delta    sigma   weight residual
     116.30  134.32  -18.02 3.50e+00 8.16e-02 2.65e+01
  angle pdb=" C   VAL A  91 "
        pdb=" CA  VAL A  91 "
        pdb=" CB  VAL A  91 "
      ideal   model   delta    sigma   weight residual
     112.45  118.70   -6.25 1.24e+00 6.50e-01 2.54e+01
  angle pdb=" CA  LEU B 376 "
        pdb=" CB  LEU B 376 "
        pdb=" CG  LEU B 376 "
      ideal   model   delta    sigma   weight residual
     116.30  133.57  -17.27 3.50e+00 8.16e-02 2.43e+01
  angle pdb=" C   ASP B 547 "
        pdb=" N   ASP B 548 "
        pdb=" CA  ASP B 548 "
      ideal   model   delta    sigma   weight residual
     122.07  128.85   -6.78 1.43e+00 4.89e-01 2.25e+01
  ... (remaining 12535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 5246
       17.19 -    34.37: 365
       34.37 -    51.55: 83
       51.55 -    68.74: 15
       68.74 -    85.92: 7
  Dihedral angle restraints: 5716
    sinusoidal: 2418
      harmonic: 3298
  Sorted by residual:
  dihedral pdb=" CA  ARG B 425 "
           pdb=" C   ARG B 425 "
           pdb=" N   ARG B 426 "
           pdb=" CA  ARG B 426 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.50  -31.50     0      5.00e+00 4.00e-02 3.97e+01
  dihedral pdb=" CA  MET B  98 "
           pdb=" C   MET B  98 "
           pdb=" N   ASN B  99 "
           pdb=" CA  ASN B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.12  -29.88     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  ARG B 355 "
           pdb=" C   ARG B 355 "
           pdb=" N   PRO B 356 "
           pdb=" CA  PRO B 356 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.95  -27.05     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 5713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1138
       0.077 -    0.155: 233
       0.155 -    0.232: 39
       0.232 -    0.310: 11
       0.310 -    0.387: 5
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  ILE B 404 "
            pdb=" CA  ILE B 404 "
            pdb=" CG1 ILE B 404 "
            pdb=" CG2 ILE B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" CB  VAL B 108 "
            pdb=" CA  VAL B 108 "
            pdb=" CG1 VAL B 108 "
            pdb=" CG2 VAL B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CB  THR B 466 "
            pdb=" CA  THR B 466 "
            pdb=" OG1 THR B 466 "
            pdb=" CG2 THR B 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 461 "    0.039 2.00e-02 2.50e+03   3.58e-02 1.60e+01
        pdb=" CG  ASN B 461 "   -0.053 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 461 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 461 "   -0.029 2.00e-02 2.50e+03
        pdb=" C1  NAG B 703 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 115 "   -0.066 5.00e-02 4.00e+02   9.95e-02 1.58e+01
        pdb=" N   PRO B 116 "    0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 115 "    0.060 5.00e-02 4.00e+02   9.12e-02 1.33e+01
        pdb=" N   PRO A 116 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 116 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 116 "    0.051 5.00e-02 4.00e+02
  ... (remaining 1641 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3127
        2.89 -     3.39: 6293
        3.39 -     3.90: 15071
        3.90 -     4.40: 14943
        4.40 -     4.90: 27349
  Nonbonded interactions: 66783
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 591 "
            pdb=" OD1 ASP B 594 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG1 THR A 591 "
            pdb=" OD1 ASP A 594 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" OG1 THR B 563 "
            pdb=" OG1 THR B 573 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" OG  SER A 136 "
            pdb=" OE1 GLU A 138 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" OG  SER B 136 "
            pdb=" OE1 GLU B 138 "
     model   vdw
     2.414 3.040
  ... (remaining 66778 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     29.470
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5751
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.152   9218  Z= 0.741
  Angle     :  1.264  18.022  12540  Z= 0.681
  Chirality :  0.070   0.387   1426
  Planarity :  0.010   0.100   1634
  Dihedral  : 12.938  85.924   3552
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.42 (0.23), residues: 1142
  helix:  None (None), residues: 0
  sheet: -0.31 (0.20), residues: 594
  loop : -1.64 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP A 346 
 HIS   0.014   0.002   HIS B 534 
 PHE   0.031   0.003   PHE A 493 
 TYR   0.034   0.003   TYR B 393 
 ARG   0.009   0.001   ARG B 425 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ASN cc_start: 0.5727 (m110) cc_final: 0.5387 (m110)
REVERT: A  328 GLU cc_start: 0.6397 (mp0) cc_final: 0.6062 (mp0)
REVERT: A  359 ARG cc_start: 0.7784 (tmm160) cc_final: 0.7389 (ttp-110)
REVERT: B   75 MET cc_start: 0.7015 (ttt) cc_final: 0.6617 (ttt)
REVERT: B  367 LEU cc_start: 0.4956 (tp) cc_final: 0.4152 (tp)
REVERT: B  409 GLU cc_start: 0.7198 (tt0) cc_final: 0.6951 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2744
  time to fit residues: 45.8632
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0370
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.4656

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
A 324 GLN
A 326 GLN
B 104 GLN
B 324 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.257250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.222891 restraints weight = 12380.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.221547 restraints weight = 17846.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.223823 restraints weight = 13871.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5763
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9218  Z= 0.254
  Angle     :  0.604  12.063  12540  Z= 0.310
  Chirality :  0.044   0.226   1426
  Planarity :  0.006   0.064   1634
  Dihedral  :  5.952  35.327   1450
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.61 %
    Favored  : 93.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.90 (0.24), residues: 1142
  helix: -5.23 (0.24), residues: 12
  sheet:  0.06 (0.20), residues: 582
  loop : -1.19 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 401 
 PHE   0.012   0.001   PHE B 245 
 TYR   0.010   0.001   TYR A 486 
 ARG   0.004   0.000   ARG B 425 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3433 (mpp) cc_final: 0.2538 (pmm)
REVERT: A  255 GLN cc_start: 0.6899 (mp10) cc_final: 0.6663 (mp10)
REVERT: B  346 TRP cc_start: 0.7565 (m-10) cc_final: 0.5942 (m-10)
REVERT: B  457 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6352 (pp20)
REVERT: B  459 LEU cc_start: 0.8128 (mt) cc_final: 0.7908 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 129
  average time/residue: 0.2794
  time to fit residues: 47.0256
Evaluate side-chains
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  457 GLU
Chi-restraints excluded: chain B residue  496 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 73 optimal weight:    0.0570
   chunk 64 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.6298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.254405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.218003 restraints weight = 12308.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.215865 restraints weight = 16885.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.217959 restraints weight = 14178.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5879
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9218  Z= 0.308
  Angle     :  0.589   7.504  12540  Z= 0.302
  Chirality :  0.044   0.177   1426
  Planarity :  0.005   0.058   1634
  Dihedral  :  5.291  32.491   1450
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.94 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.59 (0.24), residues: 1142
  helix: -5.30 (0.21), residues: 12
  sheet:  0.19 (0.21), residues: 572
  loop : -0.85 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 346 
 HIS   0.006   0.001   HIS B 401 
 PHE   0.014   0.001   PHE A 245 
 TYR   0.012   0.001   TYR A 486 
 ARG   0.008   0.000   ARG A 345 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3655 (mpp) cc_final: 0.2642 (pmm)
REVERT: B   79 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6870 (tt0)
REVERT: B  485 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7704 (mtpp)
  outliers start: 13
  outliers final: 10
  residues processed: 128
  average time/residue: 0.2943
  time to fit residues: 48.6650
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  588 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  457 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 111 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.257762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.222790 restraints weight = 11732.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.224120 restraints weight = 17510.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.224981 restraints weight = 15364.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5830
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   9218  Z= 0.410
  Angle     :  0.626   7.977  12540  Z= 0.319
  Chirality :  0.045   0.186   1426
  Planarity :  0.005   0.060   1634
  Dihedral  :  5.331  30.210   1450
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  9.36 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.56 (0.24), residues: 1142
  helix: -5.35 (0.19), residues: 12
  sheet:  0.20 (0.21), residues: 548
  loop : -0.78 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  73 
 HIS   0.007   0.001   HIS B 401 
 PHE   0.016   0.001   PHE A 245 
 TYR   0.013   0.002   TYR A 486 
 ARG   0.005   0.000   ARG B 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3653 (mpp) cc_final: 0.2990 (pmm)
REVERT: A  482 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5891 (t0)
REVERT: B   80 MET cc_start: 0.5778 (ppp) cc_final: 0.4383 (ptt)
REVERT: B  365 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6078 (pt0)
REVERT: B  485 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7659 (mtpp)
  outliers start: 18
  outliers final: 11
  residues processed: 117
  average time/residue: 0.3049
  time to fit residues: 45.9073
Evaluate side-chains
  122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  365 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 91 optimal weight:    0.1980
   chunk 44 optimal weight:    0.2980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0870
   chunk 69 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0020
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.2166

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.256067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.221501 restraints weight = 12440.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.220210 restraints weight = 17448.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.222864 restraints weight = 13365.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5797
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9218  Z= 0.160
  Angle     :  0.522   8.406  12540  Z= 0.265
  Chirality :  0.042   0.150   1426
  Planarity :  0.004   0.052   1634
  Dihedral  :  4.768  31.483   1450
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.50 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.34 (0.25), residues: 1142
  helix: -5.33 (0.20), residues: 12
  sheet:  0.31 (0.21), residues: 540
  loop : -0.56 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  73 
 HIS   0.002   0.000   HIS B 160 
 PHE   0.009   0.001   PHE B 245 
 TYR   0.010   0.001   TYR B 109 
 ARG   0.005   0.000   ARG B 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3862 (mpp) cc_final: 0.3293 (pmm)
REVERT: A  328 GLU cc_start: 0.6095 (mp0) cc_final: 0.5836 (mt-10)
REVERT: A  345 ARG cc_start: 0.6748 (mtp85) cc_final: 0.6511 (ttm-80)
REVERT: A  381 ARG cc_start: 0.6686 (mtm110) cc_final: 0.6400 (mpp80)
REVERT: A  482 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5910 (t0)
REVERT: B  123 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7379 (ttp80)
REVERT: B  457 GLU cc_start: 0.7208 (pp20) cc_final: 0.6650 (pp20)
REVERT: B  485 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7550 (mtpp)
  outliers start: 20
  outliers final: 14
  residues processed: 123
  average time/residue: 0.3157
  time to fit residues: 49.4446
Evaluate side-chains
  129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  485 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    0.0020
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0970
   chunk 22 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.257143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.222890 restraints weight = 12044.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.221313 restraints weight = 17096.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.223155 restraints weight = 14191.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5827
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9218  Z= 0.210
  Angle     :  0.534  10.335  12540  Z= 0.268
  Chirality :  0.042   0.159   1426
  Planarity :  0.004   0.041   1634
  Dihedral  :  4.698  31.626   1450
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.64 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.21 (0.25), residues: 1142
  helix: -5.32 (0.21), residues: 12
  sheet:  0.43 (0.22), residues: 534
  loop : -0.50 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  73 
 HIS   0.003   0.000   HIS B 401 
 PHE   0.011   0.001   PHE B 245 
 TYR   0.010   0.001   TYR A 486 
 ARG   0.007   0.000   ARG A 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3516 (mpp) cc_final: 0.2955 (pmm)
REVERT: A  345 ARG cc_start: 0.6700 (mtp85) cc_final: 0.6452 (ttm-80)
REVERT: A  381 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6407 (mpp80)
REVERT: A  465 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7130 (m)
REVERT: A  482 ASP cc_start: 0.6178 (OUTLIER) cc_final: 0.5897 (t0)
REVERT: A  537 THR cc_start: 0.7253 (p) cc_final: 0.6524 (t)
REVERT: B  123 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7343 (ttp80)
REVERT: B  457 GLU cc_start: 0.7221 (pp20) cc_final: 0.6727 (pp20)
REVERT: B  476 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7003 (mtt90)
REVERT: B  485 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7662 (mtpp)
  outliers start: 21
  outliers final: 16
  residues processed: 121
  average time/residue: 0.3476
  time to fit residues: 56.0526
Evaluate side-chains
  135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 93 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 108 optimal weight:    0.0980
   chunk 54 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.258726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.225749 restraints weight = 12294.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.223682 restraints weight = 16308.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.225836 restraints weight = 14779.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5807
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9218  Z= 0.214
  Angle     :  0.534  11.893  12540  Z= 0.266
  Chirality :  0.042   0.167   1426
  Planarity :  0.004   0.042   1634
  Dihedral  :  4.654  32.581   1450
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.16 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.16 (0.25), residues: 1142
  helix: -5.30 (0.21), residues: 12
  sheet:  0.42 (0.22), residues: 532
  loop : -0.42 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.010   0.001   PHE B 245 
 TYR   0.014   0.001   TYR B 109 
 ARG   0.007   0.000   ARG A 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3455 (mpp) cc_final: 0.2954 (pmm)
REVERT: A  345 ARG cc_start: 0.6704 (mtp85) cc_final: 0.6449 (ttm-80)
REVERT: A  381 ARG cc_start: 0.6757 (mtm110) cc_final: 0.6495 (mpp80)
REVERT: A  482 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5944 (t0)
REVERT: A  537 THR cc_start: 0.7181 (p) cc_final: 0.6371 (t)
REVERT: B  123 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7372 (ttp80)
REVERT: B  357 THR cc_start: 0.7583 (t) cc_final: 0.7299 (p)
REVERT: B  457 GLU cc_start: 0.7208 (pp20) cc_final: 0.6739 (pp20)
REVERT: B  485 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7597 (mtpp)
  outliers start: 20
  outliers final: 16
  residues processed: 121
  average time/residue: 0.3187
  time to fit residues: 51.6302
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 107 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 113 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 34 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9990
   chunk 70 optimal weight:    7.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
A 228 ASN
** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.259565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.226556 restraints weight = 12261.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.225274 restraints weight = 17312.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.226906 restraints weight = 15251.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5837
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9218  Z= 0.322
  Angle     :  0.589  12.905  12540  Z= 0.292
  Chirality :  0.043   0.188   1426
  Planarity :  0.004   0.040   1634
  Dihedral  :  4.895  32.131   1450
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.47 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.29 (0.25), residues: 1142
  helix: -5.30 (0.21), residues: 12
  sheet:  0.33 (0.22), residues: 532
  loop : -0.50 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  73 
 HIS   0.005   0.001   HIS B 401 
 PHE   0.013   0.001   PHE A 245 
 TYR   0.022   0.002   TYR B 109 
 ARG   0.008   0.000   ARG A 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3816 (mpp) cc_final: 0.3386 (pmm)
REVERT: A  399 ASN cc_start: 0.8013 (p0) cc_final: 0.7670 (p0)
REVERT: A  482 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.6026 (t0)
REVERT: B   80 MET cc_start: 0.5761 (ppp) cc_final: 0.4420 (ptt)
REVERT: B  357 THR cc_start: 0.7768 (t) cc_final: 0.7469 (p)
REVERT: B  457 GLU cc_start: 0.7264 (pp20) cc_final: 0.6817 (pp20)
REVERT: B  485 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7712 (mtpp)
REVERT: B  491 GLU cc_start: 0.6972 (tp30) cc_final: 0.6764 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 121
  average time/residue: 0.2739
  time to fit residues: 43.3160
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  590 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    0.0670
   chunk 30 optimal weight:    0.0070
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 102 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 105 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
A 228 ASN
** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.254859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.218344 restraints weight = 12630.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.216550 restraints weight = 16388.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.220580 restraints weight = 12683.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.4467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9218  Z= 0.208
  Angle     :  0.545  13.846  12540  Z= 0.270
  Chirality :  0.042   0.158   1426
  Planarity :  0.004   0.059   1634
  Dihedral  :  4.680  34.041   1450
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.27 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.20 (0.25), residues: 1142
  helix: -5.29 (0.22), residues: 12
  sheet:  0.37 (0.22), residues: 542
  loop : -0.43 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 360 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.010   0.001   PHE B 245 
 TYR   0.024   0.001   TYR B 109 
 ARG   0.008   0.000   ARG B 359 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3853 (mpp) cc_final: 0.3395 (pmm)
REVERT: A  345 ARG cc_start: 0.6710 (mtp85) cc_final: 0.6505 (ttm-80)
REVERT: A  381 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6463 (mpp80)
REVERT: A  399 ASN cc_start: 0.7873 (p0) cc_final: 0.7545 (p0)
REVERT: A  537 THR cc_start: 0.7122 (p) cc_final: 0.6439 (t)
REVERT: B   79 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6797 (tt0)
REVERT: B  485 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7564 (mtpp)
  outliers start: 21
  outliers final: 19
  residues processed: 118
  average time/residue: 0.3644
  time to fit residues: 56.8402
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 3.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  590 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0970
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0000
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
A 228 ASN
** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.261362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.227897 restraints weight = 12265.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.220850 restraints weight = 12581.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.222662 restraints weight = 13344.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9218  Z= 0.206
  Angle     :  0.547  14.515  12540  Z= 0.270
  Chirality :  0.042   0.159   1426
  Planarity :  0.004   0.042   1634
  Dihedral  :  4.592  33.718   1450
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.89 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    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: -0.15 (0.25), residues: 1142
  helix: -5.28 (0.23), residues: 12
  sheet:  0.40 (0.22), residues: 544
  loop : -0.40 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.010   0.001   PHE B 245 
 TYR   0.021   0.001   TYR B 109 
 ARG   0.009   0.000   ARG B 123 

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3996 (mpp) cc_final: 0.3368 (pmm)
REVERT: A  328 GLU cc_start: 0.6152 (mp0) cc_final: 0.5918 (mt-10)
REVERT: A  345 ARG cc_start: 0.6668 (mtp85) cc_final: 0.6461 (mmm160)
REVERT: A  537 THR cc_start: 0.7175 (p) cc_final: 0.6273 (t)
REVERT: B  357 THR cc_start: 0.7595 (t) cc_final: 0.7290 (p)
REVERT: B  485 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7782 (mtpp)
REVERT: B  491 GLU cc_start: 0.6885 (tp30) cc_final: 0.6680 (tp30)
  outliers start: 17
  outliers final: 16
  residues processed: 116
  average time/residue: 0.3245
  time to fit residues: 49.3203
Evaluate side-chains
  127 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  425 ARG
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 95 optimal weight:    0.0370
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   chunk 9 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.260689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.224825 restraints weight = 12055.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.217103 restraints weight = 11459.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.219239 restraints weight = 12680.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9218  Z= 0.235
  Angle     :  0.557  14.413  12540  Z= 0.275
  Chirality :  0.042   0.162   1426
  Planarity :  0.004   0.042   1634
  Dihedral  :  4.623  33.402   1450
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.37 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1142
  helix: -5.28 (0.22), residues: 12
  sheet:  0.33 (0.22), residues: 550
  loop : -0.36 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  73 
 HIS   0.004   0.001   HIS B 401 
 PHE   0.011   0.001   PHE B 245 
 TYR   0.020   0.001   TYR B 109 
 ARG   0.009   0.000   ARG B 359 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3260.40 seconds
wall clock time: 59 minutes 47.94 seconds (3587.94 seconds total)