Starting phenix.real_space_refine
on Fri Feb 14 23:28:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5v4s_8633/02_2025/5v4s_8633.cif"
  }
  resolution = 4.2
  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=   0.003
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      24      5.16       5
     C    6992      2.51       5
     N    1844      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10756
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 2689
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 132}
          Link IDs: {'PTRANS': 10, 'TRANS': 376}
          Chain breaks: 3
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 456
          Unresolved non-hydrogen angles: 579
          Unresolved non-hydrogen dihedrals: 366
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 239
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.10, per 1000 atoms: 0.47
  Number of scatterers: 10756
  At special positions: 0
  Unit cell: (116.067, 116.067, 109.24, 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      24     16.00
     O    1896      8.00
     N    1844      7.00
     C    6992      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: 3.01
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2936

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 8 sheets defined
      74.2% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 27
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE A  31 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 59
    Processing helix  chain 'A' and resid 84 through 93
    Processing helix  chain 'A' and resid 95 through 104
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU A 124 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LYS A 125 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 141
      removed outlier: 4.024A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
    Processing helix  chain 'A' and resid 179 through 195
    Processing helix  chain 'A' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 290
    Processing helix  chain 'A' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU A 310 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 319 through 330
    Processing helix  chain 'A' and resid 380 through 386
    Processing helix  chain 'A' and resid 407 through 417
    Processing helix  chain 'A' and resid 417 through 429
      removed outlier: 3.884A  pdb=" N   ILE A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 429 " --> pdb=" O   GLU A 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 27
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE B  31 " --> pdb=" O   PRO B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 59
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 95 through 104
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU B 124 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS B 125 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 173
    Processing helix  chain 'B' and resid 179 through 195
    Processing helix  chain 'B' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET B 249 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 290
    Processing helix  chain 'B' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B 310 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 319 through 330
    Processing helix  chain 'B' and resid 380 through 386
    Processing helix  chain 'B' and resid 407 through 417
    Processing helix  chain 'B' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER B 427 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 429 " --> pdb=" O   GLU B 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 27
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE C  31 " --> pdb=" O   PRO C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 59
    Processing helix  chain 'C' and resid 84 through 93
    Processing helix  chain 'C' and resid 95 through 104
    Processing helix  chain 'C' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL C 120 " --> pdb=" O   LEU C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU C 124 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS C 125 " --> pdb=" O   ARG C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 173
    Processing helix  chain 'C' and resid 179 through 195
    Processing helix  chain 'C' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET C 249 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG C 268 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 290
    Processing helix  chain 'C' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU C 308 " --> pdb=" O   LEU C 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU C 310 " --> pdb=" O   ARG C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 317
    Processing helix  chain 'C' and resid 319 through 330
    Processing helix  chain 'C' and resid 380 through 386
    Processing helix  chain 'C' and resid 407 through 417
    Processing helix  chain 'C' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE C 424 " --> pdb=" O   PHE C 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER C 427 " --> pdb=" O   ALA C 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 429 " --> pdb=" O   GLU C 425 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 27
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE D  31 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 59
    Processing helix  chain 'D' and resid 84 through 93
    Processing helix  chain 'D' and resid 95 through 104
    Processing helix  chain 'D' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL D 120 " --> pdb=" O   LEU D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU D 124 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS D 125 " --> pdb=" O   ARG D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN D 134 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 173
    Processing helix  chain 'D' and resid 179 through 195
    Processing helix  chain 'D' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET D 249 " --> pdb=" O   GLN D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG D 268 " --> pdb=" O   ASN D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 290
    Processing helix  chain 'D' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU D 308 " --> pdb=" O   LEU D 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU D 310 " --> pdb=" O   ARG D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 317
    Processing helix  chain 'D' and resid 319 through 330
    Processing helix  chain 'D' and resid 380 through 386
    Processing helix  chain 'D' and resid 407 through 417
    Processing helix  chain 'D' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE D 424 " --> pdb=" O   PHE D 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER D 427 " --> pdb=" O   ALA D 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA D 429 " --> pdb=" O   GLU D 425 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU A 401 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342
      removed outlier: 6.530A  pdb=" N   THR A 340 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA A 396 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU B 401 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR B 340 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA B 396 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU C 401 " --> pdb=" O   SER C 355 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR C 340 " --> pdb=" O   ALA C 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA C 396 " --> pdb=" O   THR C 340 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU D 401 " --> pdb=" O   SER D 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR D 340 " --> pdb=" O   ALA D 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA D 396 " --> pdb=" O   THR D 340 " (cutoff:3.500A)

    893 hydrogen bonds defined for protein.
    2595 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: 3.70

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2224
        1.32 -     1.44: 2731
        1.44 -     1.56: 5969
        1.56 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 10960
  Sorted by residual:
  bond pdb=" CA  LEU A 322 "
       pdb=" C   LEU A 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.049 1.27e-02 6.20e+03 1.46e+01
  bond pdb=" CA  LEU B 322 "
       pdb=" C   LEU B 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.048 1.27e-02 6.20e+03 1.45e+01
  bond pdb=" CA  LEU C 322 "
       pdb=" C   LEU C 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.048 1.27e-02 6.20e+03 1.45e+01
  bond pdb=" CA  LEU D 322 "
       pdb=" C   LEU D 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.048 1.27e-02 6.20e+03 1.45e+01
  bond pdb=" N   PRO C 144 "
       pdb=" CD  PRO C 144 "
    ideal  model  delta    sigma   weight residual
    1.473  1.431  0.042 1.40e-02 5.10e+03 8.93e+00
  ... (remaining 10955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.59: 14968
        6.59 -    13.19: 48
       13.19 -    19.78: 8
       19.78 -    26.37: 8
       26.37 -    32.96: 4
  Bond angle restraints: 15036
  Sorted by residual:
  angle pdb=" N   LEU B  96 "
        pdb=" CA  LEU B  96 "
        pdb=" C   LEU B  96 "
      ideal   model   delta    sigma   weight residual
     110.80  143.76  -32.96 2.13e+00 2.20e-01 2.39e+02
  angle pdb=" N   LEU C  96 "
        pdb=" CA  LEU C  96 "
        pdb=" C   LEU C  96 "
      ideal   model   delta    sigma   weight residual
     110.80  143.76  -32.96 2.13e+00 2.20e-01 2.39e+02
  angle pdb=" N   LEU D  96 "
        pdb=" CA  LEU D  96 "
        pdb=" C   LEU D  96 "
      ideal   model   delta    sigma   weight residual
     110.80  143.76  -32.96 2.13e+00 2.20e-01 2.39e+02
  angle pdb=" N   LEU A  96 "
        pdb=" CA  LEU A  96 "
        pdb=" C   LEU A  96 "
      ideal   model   delta    sigma   weight residual
     110.80  143.75  -32.95 2.13e+00 2.20e-01 2.39e+02
  angle pdb=" N   GLU C  97 "
        pdb=" CA  GLU C  97 "
        pdb=" CB  GLU C  97 "
      ideal   model   delta    sigma   weight residual
     110.07   89.00   21.07 1.45e+00 4.76e-01 2.11e+02
  ... (remaining 15031 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.27: 6012
       13.27 -    26.54: 180
       26.54 -    39.81: 60
       39.81 -    53.07: 12
       53.07 -    66.34: 12
  Dihedral angle restraints: 6276
    sinusoidal: 1748
      harmonic: 4528
  Sorted by residual:
  dihedral pdb=" C   ARG C  30 "
           pdb=" N   ARG C  30 "
           pdb=" CA  ARG C  30 "
           pdb=" CB  ARG C  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.91   31.31     0      2.50e+00 1.60e-01 1.57e+02
  dihedral pdb=" C   ARG D  30 "
           pdb=" N   ARG D  30 "
           pdb=" CA  ARG D  30 "
           pdb=" CB  ARG D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.91   31.31     0      2.50e+00 1.60e-01 1.57e+02
  dihedral pdb=" C   ARG B  30 "
           pdb=" N   ARG B  30 "
           pdb=" CA  ARG B  30 "
           pdb=" CB  ARG B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.91   31.31     0      2.50e+00 1.60e-01 1.57e+02
  ... (remaining 6273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.300: 1816
       0.300 -    0.599: 12
       0.599 -    0.899: 4
       0.899 -    1.199: 0
       1.199 -    1.499: 12
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" CA  LEU A  96 "
            pdb=" N   LEU A  96 "
            pdb=" C   LEU A  96 "
            pdb=" CB  LEU A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.01    1.50 2.00e-01 2.50e+01 5.62e+01
  chirality pdb=" CA  LEU D  96 "
            pdb=" N   LEU D  96 "
            pdb=" C   LEU D  96 "
            pdb=" CB  LEU D  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.01    1.50 2.00e-01 2.50e+01 5.60e+01
  chirality pdb=" CA  LEU B  96 "
            pdb=" N   LEU B  96 "
            pdb=" C   LEU B  96 "
            pdb=" CB  LEU B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.01    1.50 2.00e-01 2.50e+01 5.60e+01
  ... (remaining 1841 not shown)

  Planarity restraints: 1888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 141 "    0.085 5.00e-02 4.00e+02   1.29e-01 2.65e+01
        pdb=" N   PRO D 142 "   -0.223 5.00e-02 4.00e+02
        pdb=" CA  PRO D 142 "    0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO D 142 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 141 "    0.085 5.00e-02 4.00e+02   1.29e-01 2.65e+01
        pdb=" N   PRO C 142 "   -0.223 5.00e-02 4.00e+02
        pdb=" CA  PRO C 142 "    0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO C 142 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 141 "   -0.085 5.00e-02 4.00e+02   1.29e-01 2.65e+01
        pdb=" N   PRO B 142 "    0.223 5.00e-02 4.00e+02
        pdb=" CA  PRO B 142 "   -0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO B 142 "   -0.066 5.00e-02 4.00e+02
  ... (remaining 1885 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4445
        2.86 -     3.37: 12000
        3.37 -     3.88: 17535
        3.88 -     4.39: 20739
        4.39 -     4.90: 30705
  Nonbonded interactions: 85424
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 101 "
            pdb=" OH  TYR A 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR D 101 "
            pdb=" OH  TYR D 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR C 101 "
            pdb=" OH  TYR C 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR B 101 "
            pdb=" OH  TYR B 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   ALA A 195 "
            pdb=" OG1 THR A 196 "
     model   vdw
     2.436 3.040
  ... (remaining 85419 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 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     25.560
  Find NCS groups from input model:        0.220
  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:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
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      :  0.012   0.062  10960  Z= 0.792
  Angle     :  1.557  32.963  15036  Z= 1.038
  Chirality :  0.138   1.499   1844
  Planarity :  0.011   0.129   1888
  Dihedral  :  8.803  66.342   3340
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.60 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.36 %
  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: -1.95 (0.19), residues: 1516
  helix: -0.89 (0.13), residues: 1068
  sheet: -1.20 (0.47), residues: 68
  loop : -2.00 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP C  58 
 HIS   0.002   0.002   HIS D 161 
 PHE   0.011   0.002   PHE D  21 
 TYR   0.034   0.005   TYR A 272 
 ARG   0.003   0.001   ARG C  30 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ASN cc_start: 0.8099 (m-40) cc_final: 0.7890 (t0)
REVERT: C  230 ASN cc_start: 0.8120 (m-40) cc_final: 0.7902 (t0)
REVERT: D  230 ASN cc_start: 0.8098 (m-40) cc_final: 0.7813 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2905
  time to fit residues: 59.2562
Evaluate side-chains
  83 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 119 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 138 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
B 134 GLN
C 134 GLN
D 134 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.053684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.042972 restraints weight = 89973.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.043342 restraints weight = 69567.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.043998 restraints weight = 61755.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10960  Z= 0.229
  Angle     :  0.571   6.875  15036  Z= 0.332
  Chirality :  0.040   0.142   1844
  Planarity :  0.005   0.063   1888
  Dihedral  :  4.216  15.615   1652
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  3.17 %
    Favored  : 96.34 %
  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:  0.69 (0.20), residues: 1516
  helix:  0.93 (0.15), residues: 1100
  sheet:  0.36 (0.67), residues: 52
  loop : -0.77 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 167 
 HIS   0.001   0.000   HIS B 161 
 PHE   0.020   0.002   PHE C 152 
 TYR   0.020   0.002   TYR B 272 
 ARG   0.003   0.001   ARG A 246 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 ASN cc_start: 0.9379 (m-40) cc_final: 0.8763 (t0)
REVERT: A  274 MET cc_start: 0.9663 (mtm) cc_final: 0.9443 (ptp)
REVERT: B  274 MET cc_start: 0.9658 (mtm) cc_final: 0.9437 (ptp)
REVERT: C  230 ASN cc_start: 0.9435 (m-40) cc_final: 0.8853 (t0)
REVERT: C  274 MET cc_start: 0.9661 (mtm) cc_final: 0.9438 (ptp)
REVERT: D  230 ASN cc_start: 0.9358 (m-40) cc_final: 0.8859 (t0)
REVERT: D  274 MET cc_start: 0.9654 (mtm) cc_final: 0.9434 (ptp)
  outliers start: 4
  outliers final: 0
  residues processed: 118
  average time/residue: 0.3072
  time to fit residues: 48.0197
Evaluate side-chains
  73 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 112 optimal weight:    9.9990
   chunk 141 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 135 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 70 optimal weight:   30.0000
   chunk 111 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.051947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.040873 restraints weight = 100220.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.041442 restraints weight = 79462.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.041829 restraints weight = 66662.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10960  Z= 0.323
  Angle     :  0.642   6.820  15036  Z= 0.375
  Chirality :  0.041   0.152   1844
  Planarity :  0.006   0.046   1888
  Dihedral  :  4.318  15.415   1652
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.21), residues: 1516
  helix:  1.11 (0.15), residues: 1096
  sheet:  1.33 (0.80), residues: 48
  loop : -0.20 (0.36), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 162 
 HIS   0.004   0.003   HIS B 161 
 PHE   0.027   0.002   PHE D 154 
 TYR   0.026   0.002   TYR D 272 
 ARG   0.005   0.001   ARG B 148 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9684 (ptmt) cc_final: 0.9400 (ptmt)
REVERT: A  217 MET cc_start: 0.9542 (mtm) cc_final: 0.9327 (ptp)
REVERT: B  125 LYS cc_start: 0.9668 (ptmt) cc_final: 0.9378 (ptmt)
REVERT: B  217 MET cc_start: 0.9516 (mtm) cc_final: 0.9295 (ptp)
REVERT: C  125 LYS cc_start: 0.9685 (ptmt) cc_final: 0.9384 (ptmt)
REVERT: C  217 MET cc_start: 0.9539 (mtm) cc_final: 0.9333 (mtp)
REVERT: D  125 LYS cc_start: 0.9786 (tptp) cc_final: 0.9529 (tppp)
REVERT: D  217 MET cc_start: 0.9531 (mtm) cc_final: 0.9315 (ptp)
REVERT: D  230 ASN cc_start: 0.9637 (m-40) cc_final: 0.9287 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2847
  time to fit residues: 38.3877
Evaluate side-chains
  67 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 113 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 144 optimal weight:   50.0000
   chunk 118 optimal weight:    0.0370
   chunk 94 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 106 optimal weight:   50.0000
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
** D 230 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 = 0.3407 r_free = 0.3407 target = 0.055437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.043395 restraints weight = 83048.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.044189 restraints weight = 62885.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.044789 restraints weight = 50690.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064  10960  Z= 0.170
  Angle     :  0.462   4.904  15036  Z= 0.264
  Chirality :  0.037   0.130   1844
  Planarity :  0.003   0.034   1888
  Dihedral  :  3.893  15.374   1652
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    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:  1.83 (0.21), residues: 1516
  helix:  1.67 (0.15), residues: 1112
  sheet:  1.72 (0.83), residues: 48
  loop : -0.20 (0.36), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 162 
 HIS   0.001   0.000   HIS C 161 
 PHE   0.026   0.002   PHE D 154 
 TYR   0.017   0.001   TYR A 272 
 ARG   0.002   0.000   ARG D 148 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9608 (ptmt) cc_final: 0.9348 (ptmt)
REVERT: A  230 ASN cc_start: 0.9658 (m110) cc_final: 0.9351 (t0)
REVERT: A  274 MET cc_start: 0.9703 (mtm) cc_final: 0.9416 (ptp)
REVERT: B  125 LYS cc_start: 0.9592 (ptmt) cc_final: 0.9326 (ptmt)
REVERT: B  274 MET cc_start: 0.9699 (mtm) cc_final: 0.9433 (ptp)
REVERT: C  125 LYS cc_start: 0.9619 (ptmt) cc_final: 0.9350 (ptmt)
REVERT: C  230 ASN cc_start: 0.9652 (m110) cc_final: 0.9302 (t0)
REVERT: C  274 MET cc_start: 0.9702 (mtm) cc_final: 0.9431 (ptp)
REVERT: D  125 LYS cc_start: 0.9778 (tptp) cc_final: 0.9169 (tppp)
REVERT: D  230 ASN cc_start: 0.9657 (m-40) cc_final: 0.9191 (t0)
REVERT: D  274 MET cc_start: 0.9697 (mtm) cc_final: 0.9402 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2995
  time to fit residues: 41.8787
Evaluate side-chains
  60 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 144 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 104 optimal weight:   50.0000
   chunk 136 optimal weight:    9.9990
   chunk 123 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 114 optimal weight:   20.0000
   chunk 55 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B  59 ASN
D 230 ASN
** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.052784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.041734 restraints weight = 100657.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.042315 restraints weight = 77223.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.042769 restraints weight = 63851.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10960  Z= 0.232
  Angle     :  0.510   5.077  15036  Z= 0.297
  Chirality :  0.039   0.148   1844
  Planarity :  0.004   0.032   1888
  Dihedral  :  3.877  15.811   1652
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  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:  2.08 (0.22), residues: 1516
  helix:  1.80 (0.15), residues: 1108
  sheet:  2.08 (0.86), residues: 48
  loop :  0.07 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 162 
 HIS   0.003   0.001   HIS C 161 
 PHE   0.025   0.002   PHE D 154 
 TYR   0.017   0.002   TYR B 272 
 ARG   0.006   0.001   ARG D 148 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9658 (ptmt) cc_final: 0.9343 (ptmt)
REVERT: A  162 TRP cc_start: 0.9268 (m-90) cc_final: 0.8974 (m-90)
REVERT: A  217 MET cc_start: 0.9492 (mtm) cc_final: 0.9287 (mtp)
REVERT: A  230 ASN cc_start: 0.9689 (m110) cc_final: 0.9411 (t0)
REVERT: A  274 MET cc_start: 0.9736 (mtm) cc_final: 0.9498 (mtp)
REVERT: B  125 LYS cc_start: 0.9660 (ptmt) cc_final: 0.9354 (ptmt)
REVERT: B  162 TRP cc_start: 0.9263 (m-90) cc_final: 0.8977 (m-90)
REVERT: B  274 MET cc_start: 0.9734 (mtm) cc_final: 0.9493 (mtp)
REVERT: C  125 LYS cc_start: 0.9672 (ptmt) cc_final: 0.9356 (ptmt)
REVERT: C  162 TRP cc_start: 0.9250 (m-90) cc_final: 0.8903 (m100)
REVERT: C  230 ASN cc_start: 0.9721 (m110) cc_final: 0.9433 (t0)
REVERT: C  274 MET cc_start: 0.9729 (mtm) cc_final: 0.9437 (ptp)
REVERT: D  125 LYS cc_start: 0.9759 (tptp) cc_final: 0.9396 (mttt)
REVERT: D  162 TRP cc_start: 0.9284 (m-90) cc_final: 0.8981 (m-90)
REVERT: D  217 MET cc_start: 0.9497 (mtm) cc_final: 0.9280 (mtp)
REVERT: D  274 MET cc_start: 0.9718 (mtm) cc_final: 0.9395 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.2616
  time to fit residues: 31.9858
Evaluate side-chains
  57 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 91 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 125 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 141 GLN
C  59 ASN
C 141 GLN
C 161 HIS
D 141 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.052776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.041662 restraints weight = 105901.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.042354 restraints weight = 79093.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.042689 restraints weight = 62940.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10960  Z= 0.209
  Angle     :  0.485   5.296  15036  Z= 0.281
  Chirality :  0.038   0.119   1844
  Planarity :  0.003   0.029   1888
  Dihedral  :  3.775  16.857   1652
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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:  2.42 (0.22), residues: 1516
  helix:  2.06 (0.15), residues: 1112
  sheet:  1.91 (0.83), residues: 48
  loop :  0.17 (0.38), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 162 
 HIS   0.001   0.001   HIS B 161 
 PHE   0.022   0.002   PHE D 154 
 TYR   0.016   0.001   TYR B 272 
 ARG   0.002   0.000   ARG B 268 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9656 (ptmt) cc_final: 0.9346 (ptmt)
REVERT: A  162 TRP cc_start: 0.9302 (m-90) cc_final: 0.8903 (m-90)
REVERT: A  230 ASN cc_start: 0.9670 (m110) cc_final: 0.9309 (t0)
REVERT: A  274 MET cc_start: 0.9726 (mtm) cc_final: 0.9452 (mtp)
REVERT: B  125 LYS cc_start: 0.9638 (ptmt) cc_final: 0.9308 (ptmt)
REVERT: B  162 TRP cc_start: 0.9339 (m-90) cc_final: 0.9011 (m-90)
REVERT: B  274 MET cc_start: 0.9726 (mtm) cc_final: 0.9453 (mtp)
REVERT: C  125 LYS cc_start: 0.9662 (ptmt) cc_final: 0.9346 (ptmt)
REVERT: C  149 LEU cc_start: 0.9103 (mt) cc_final: 0.8883 (mt)
REVERT: C  162 TRP cc_start: 0.9300 (m-90) cc_final: 0.8909 (m-90)
REVERT: C  230 ASN cc_start: 0.9698 (m110) cc_final: 0.9394 (t0)
REVERT: C  274 MET cc_start: 0.9723 (mtm) cc_final: 0.9451 (mtp)
REVERT: D  162 TRP cc_start: 0.9278 (m-90) cc_final: 0.8885 (m-90)
REVERT: D  217 MET cc_start: 0.9518 (mtm) cc_final: 0.9304 (mtp)
REVERT: D  274 MET cc_start: 0.9714 (mtm) cc_final: 0.9435 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2765
  time to fit residues: 34.3629
Evaluate side-chains
  64 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 111 optimal weight:   50.0000
   chunk 81 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 107 optimal weight:   50.0000
   chunk 112 optimal weight:    5.9990
   chunk 114 optimal weight:   20.0000
   chunk 124 optimal weight:    6.9990
   chunk 33 optimal weight:   50.0000
   chunk 94 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 7 optimal weight:   20.0000
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
D 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.051961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.041590 restraints weight = 106511.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.042211 restraints weight = 80353.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.042557 restraints weight = 65051.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.6104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10960  Z= 0.289
  Angle     :  0.562   5.151  15036  Z= 0.329
  Chirality :  0.040   0.119   1844
  Planarity :  0.004   0.036   1888
  Dihedral  :  4.110  17.246   1652
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  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:  2.18 (0.22), residues: 1516
  helix:  1.81 (0.15), residues: 1112
  sheet:  1.59 (0.79), residues: 48
  loop :  0.44 (0.40), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 155 
 HIS   0.003   0.002   HIS C 161 
 PHE   0.021   0.002   PHE C 154 
 TYR   0.018   0.002   TYR B 272 
 ARG   0.002   0.001   ARG C 268 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9688 (ptmt) cc_final: 0.9323 (ptmt)
REVERT: A  149 LEU cc_start: 0.9231 (mt) cc_final: 0.9011 (mt)
REVERT: A  151 LEU cc_start: 0.9754 (mt) cc_final: 0.9538 (tp)
REVERT: A  162 TRP cc_start: 0.9518 (m-90) cc_final: 0.9086 (m-90)
REVERT: A  217 MET cc_start: 0.9493 (mtm) cc_final: 0.9289 (mtp)
REVERT: A  230 ASN cc_start: 0.9679 (m110) cc_final: 0.9264 (t0)
REVERT: A  274 MET cc_start: 0.9672 (mtm) cc_final: 0.9352 (mtp)
REVERT: B  125 LYS cc_start: 0.9669 (ptmt) cc_final: 0.9310 (ptmt)
REVERT: B  162 TRP cc_start: 0.9515 (m-90) cc_final: 0.9092 (m-90)
REVERT: B  274 MET cc_start: 0.9714 (mtm) cc_final: 0.9465 (mtp)
REVERT: C  125 LYS cc_start: 0.9676 (ptmt) cc_final: 0.9312 (ptmt)
REVERT: C  149 LEU cc_start: 0.9252 (mt) cc_final: 0.9051 (mt)
REVERT: C  162 TRP cc_start: 0.9465 (m-90) cc_final: 0.8999 (m-90)
REVERT: C  230 ASN cc_start: 0.9716 (m110) cc_final: 0.9375 (t0)
REVERT: C  274 MET cc_start: 0.9681 (mtm) cc_final: 0.9385 (mtp)
REVERT: D  162 TRP cc_start: 0.9489 (m-90) cc_final: 0.9028 (m-90)
REVERT: D  217 MET cc_start: 0.9510 (mtm) cc_final: 0.9276 (mtp)
REVERT: D  274 MET cc_start: 0.9648 (mtm) cc_final: 0.9342 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2656
  time to fit residues: 31.6112
Evaluate side-chains
  65 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 65 optimal weight:   50.0000
   chunk 96 optimal weight:    0.6980
   chunk 33 optimal weight:   50.0000
   chunk 60 optimal weight:    0.9990
   chunk 72 optimal weight:   30.0000
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.052918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.041859 restraints weight = 104024.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.042521 restraints weight = 77814.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.042999 restraints weight = 62032.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.6221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10960  Z= 0.154
  Angle     :  0.460   5.780  15036  Z= 0.261
  Chirality :  0.038   0.159   1844
  Planarity :  0.003   0.022   1888
  Dihedral  :  3.685  16.794   1652
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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:  2.79 (0.22), residues: 1516
  helix:  2.31 (0.15), residues: 1112
  sheet: -0.36 (0.63), residues: 88
  loop :  0.97 (0.43), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP C 162 
 HIS   0.003   0.002   HIS D 161 
 PHE   0.021   0.001   PHE D 154 
 TYR   0.018   0.001   TYR A 224 
 ARG   0.002   0.000   ARG B 246 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9719 (ptmt) cc_final: 0.9392 (ptmt)
REVERT: A  149 LEU cc_start: 0.9234 (mt) cc_final: 0.9015 (mt)
REVERT: A  154 PHE cc_start: 0.9460 (t80) cc_final: 0.9240 (t80)
REVERT: A  162 TRP cc_start: 0.9364 (m-90) cc_final: 0.9041 (m100)
REVERT: A  230 ASN cc_start: 0.9727 (m-40) cc_final: 0.9412 (t0)
REVERT: A  274 MET cc_start: 0.9716 (mtm) cc_final: 0.9438 (mtp)
REVERT: B  125 LYS cc_start: 0.9703 (ptmt) cc_final: 0.9378 (ptmt)
REVERT: B  162 TRP cc_start: 0.9364 (m-90) cc_final: 0.9042 (m100)
REVERT: B  274 MET cc_start: 0.9714 (mtm) cc_final: 0.9475 (mtp)
REVERT: C  125 LYS cc_start: 0.9722 (ptmt) cc_final: 0.9406 (ptmt)
REVERT: C  149 LEU cc_start: 0.9283 (mt) cc_final: 0.9072 (mt)
REVERT: C  162 TRP cc_start: 0.9326 (m-90) cc_final: 0.9014 (m100)
REVERT: C  230 ASN cc_start: 0.9758 (m110) cc_final: 0.9446 (t0)
REVERT: C  274 MET cc_start: 0.9722 (mtm) cc_final: 0.9487 (mtp)
REVERT: D  125 LYS cc_start: 0.9790 (tptp) cc_final: 0.9552 (mttt)
REVERT: D  162 TRP cc_start: 0.9331 (m-90) cc_final: 0.8997 (m100)
REVERT: D  217 MET cc_start: 0.9531 (mtm) cc_final: 0.9310 (mtp)
REVERT: D  274 MET cc_start: 0.9700 (mtm) cc_final: 0.9413 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2765
  time to fit residues: 35.6739
Evaluate side-chains
  65 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 136 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:   50.0000
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.052486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.041458 restraints weight = 108420.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.042101 restraints weight = 81338.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.042548 restraints weight = 65080.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.6447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10960  Z= 0.193
  Angle     :  0.478   6.002  15036  Z= 0.279
  Chirality :  0.038   0.139   1844
  Planarity :  0.003   0.021   1888
  Dihedral  :  3.689  16.809   1652
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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:  2.88 (0.22), residues: 1516
  helix:  2.36 (0.15), residues: 1116
  sheet: -0.38 (0.64), residues: 88
  loop :  1.09 (0.43), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP C 162 
 HIS   0.002   0.001   HIS D 161 
 PHE   0.024   0.001   PHE D 154 
 TYR   0.015   0.001   TYR A 272 
 ARG   0.002   0.000   ARG C 268 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9707 (ptmt) cc_final: 0.9393 (ptmt)
REVERT: A  154 PHE cc_start: 0.9524 (t80) cc_final: 0.9308 (t80)
REVERT: A  162 TRP cc_start: 0.9410 (m-90) cc_final: 0.9052 (m100)
REVERT: A  230 ASN cc_start: 0.9740 (m-40) cc_final: 0.9415 (t0)
REVERT: A  274 MET cc_start: 0.9697 (mtm) cc_final: 0.9464 (mtp)
REVERT: B  125 LYS cc_start: 0.9690 (ptmt) cc_final: 0.9371 (ptmt)
REVERT: B  162 TRP cc_start: 0.9433 (m-90) cc_final: 0.9080 (m100)
REVERT: B  274 MET cc_start: 0.9718 (mtm) cc_final: 0.9459 (mtp)
REVERT: C  125 LYS cc_start: 0.9710 (ptmt) cc_final: 0.9385 (ptmt)
REVERT: C  149 LEU cc_start: 0.9257 (mt) cc_final: 0.9045 (mt)
REVERT: C  162 TRP cc_start: 0.9384 (m-90) cc_final: 0.9047 (m100)
REVERT: C  230 ASN cc_start: 0.9750 (m110) cc_final: 0.9454 (t0)
REVERT: C  274 MET cc_start: 0.9730 (mtm) cc_final: 0.9473 (mtp)
REVERT: D  162 TRP cc_start: 0.9395 (m-90) cc_final: 0.9040 (m100)
REVERT: D  217 MET cc_start: 0.9525 (mtm) cc_final: 0.9295 (mtp)
REVERT: D  274 MET cc_start: 0.9686 (mtm) cc_final: 0.9447 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2707
  time to fit residues: 31.3202
Evaluate side-chains
  66 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 130 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0170
   chunk 117 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.7224

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

Flipped N/Q/H residues before XYZ refinement:
D 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.053178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.042063 restraints weight = 103225.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.042675 restraints weight = 77229.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.043151 restraints weight = 62403.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.6598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10960  Z= 0.155
  Angle     :  0.463   6.644  15036  Z= 0.264
  Chirality :  0.038   0.144   1844
  Planarity :  0.002   0.020   1888
  Dihedral  :  3.508  16.435   1652
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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:  3.02 (0.22), residues: 1516
  helix:  2.53 (0.15), residues: 1124
  sheet: -0.35 (0.65), residues: 88
  loop :  0.79 (0.43), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C 162 
 HIS   0.001   0.001   HIS C 161 
 PHE   0.021   0.001   PHE D 154 
 TYR   0.014   0.001   TYR B 272 
 ARG   0.005   0.000   ARG B 246 

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.9712 (ptmt) cc_final: 0.9400 (ptmt)
REVERT: A  149 LEU cc_start: 0.9262 (mt) cc_final: 0.9061 (mt)
REVERT: A  154 PHE cc_start: 0.9563 (t80) cc_final: 0.9322 (t80)
REVERT: A  162 TRP cc_start: 0.9372 (m-90) cc_final: 0.8913 (m100)
REVERT: A  230 ASN cc_start: 0.9747 (m-40) cc_final: 0.9409 (t0)
REVERT: A  274 MET cc_start: 0.9729 (mtm) cc_final: 0.9466 (mtp)
REVERT: B  125 LYS cc_start: 0.9701 (ptmt) cc_final: 0.9393 (ptmt)
REVERT: B  162 TRP cc_start: 0.9421 (m-90) cc_final: 0.8997 (m100)
REVERT: B  274 MET cc_start: 0.9720 (mtm) cc_final: 0.9451 (mtp)
REVERT: C  125 LYS cc_start: 0.9714 (ptmt) cc_final: 0.9398 (ptmt)
REVERT: C  149 LEU cc_start: 0.9242 (mt) cc_final: 0.9036 (mt)
REVERT: C  162 TRP cc_start: 0.9357 (m-90) cc_final: 0.8970 (m100)
REVERT: C  230 ASN cc_start: 0.9755 (m110) cc_final: 0.9468 (t0)
REVERT: C  274 MET cc_start: 0.9721 (mtm) cc_final: 0.9450 (mtp)
REVERT: D  162 TRP cc_start: 0.9327 (m-90) cc_final: 0.8883 (m100)
REVERT: D  217 MET cc_start: 0.9482 (mtm) cc_final: 0.9250 (mtp)
REVERT: D  242 LYS cc_start: 0.9506 (mppt) cc_final: 0.9263 (ptpp)
REVERT: D  274 MET cc_start: 0.9714 (mtm) cc_final: 0.9446 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2650
  time to fit residues: 30.7964
Evaluate side-chains
  68 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:   50.0000
   chunk 146 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   chunk 111 optimal weight:   50.0000
   chunk 113 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   chunk 28 optimal weight:   50.0000
   chunk 137 optimal weight:    7.9990
   chunk 144 optimal weight:   20.0000
   chunk 96 optimal weight:    0.8980
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
D 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.051810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.041306 restraints weight = 110888.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.041983 restraints weight = 83031.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.042457 restraints weight = 65928.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.6861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10960  Z= 0.245
  Angle     :  0.525   5.761  15036  Z= 0.307
  Chirality :  0.039   0.131   1844
  Planarity :  0.004   0.029   1888
  Dihedral  :  3.809  17.437   1652
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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:  2.96 (0.23), residues: 1516
  helix:  2.39 (0.15), residues: 1116
  sheet: -0.55 (0.62), residues: 88
  loop :  1.28 (0.44), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP C 162 
 HIS   0.003   0.002   HIS B 161 
 PHE   0.023   0.002   PHE C 154 
 TYR   0.017   0.002   TYR D 272 
 ARG   0.002   0.000   ARG B 122 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2727.29 seconds
wall clock time: 49 minutes 50.45 seconds (2990.45 seconds total)