Starting phenix.real_space_refine
on Mon Jul 28 22:50:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5v4s_8632/07_2025/5v4s_8632.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5v4s_8632/07_2025/5v4s_8632.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_8632/07_2025/5v4s_8632.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5v4s_8632/07_2025/5v4s_8632.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5v4s_8632/07_2025/5v4s_8632.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5v4s_8632/07_2025/5v4s_8632.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=   0.001 sd=   0.009
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-5711/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: 5.30, per 1000 atoms: 0.49
  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: 3.09
  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: 1.27
  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: 3.72

  Time building geometry restraints manager: 3.58 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:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.070
  Find NCS groups from input model:        0.280
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
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= 0.794
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17439 (  893)
  hydrogen bonds       : angle       7.07769 ( 2595)
  covalent geometry    : bond        0.01192 (10960)
  covalent geometry    : angle       1.55716 (15036)

*********************** 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
  403 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 403
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 VAL cc_start: 0.8582 (t) cc_final: 0.8307 (t)
REVERT: A   30 ARG cc_start: 0.7106 (mtt180) cc_final: 0.5941 (mmp80)
REVERT: A   88 ILE cc_start: 0.8451 (mt) cc_final: 0.8148 (mm)
REVERT: A  134 GLN cc_start: 0.8432 (tp40) cc_final: 0.8110 (tp40)
REVERT: A  249 MET cc_start: 0.8463 (ttp) cc_final: 0.8247 (ttm)
REVERT: B   10 VAL cc_start: 0.8571 (t) cc_final: 0.8288 (t)
REVERT: B   30 ARG cc_start: 0.7114 (mtt180) cc_final: 0.5910 (mmp80)
REVERT: B   88 ILE cc_start: 0.8460 (mt) cc_final: 0.8151 (mm)
REVERT: B  134 GLN cc_start: 0.8435 (tp40) cc_final: 0.8127 (tp40)
REVERT: B  249 MET cc_start: 0.8498 (ttp) cc_final: 0.8269 (ttm)
REVERT: C   10 VAL cc_start: 0.8563 (t) cc_final: 0.8280 (t)
REVERT: C   30 ARG cc_start: 0.7134 (mtt180) cc_final: 0.5893 (mmp80)
REVERT: C   88 ILE cc_start: 0.8455 (mt) cc_final: 0.8158 (mm)
REVERT: C  134 GLN cc_start: 0.8382 (tp40) cc_final: 0.8052 (tp40)
REVERT: C  249 MET cc_start: 0.8501 (ttp) cc_final: 0.8282 (ttm)
REVERT: D   10 VAL cc_start: 0.8553 (t) cc_final: 0.8264 (t)
REVERT: D   30 ARG cc_start: 0.7137 (mtt180) cc_final: 0.5934 (mmp80)
REVERT: D   88 ILE cc_start: 0.8445 (mt) cc_final: 0.8155 (mm)
REVERT: D  134 GLN cc_start: 0.8384 (tp40) cc_final: 0.8054 (tp40)
REVERT: D  249 MET cc_start: 0.8448 (ttp) cc_final: 0.8241 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 403
  average time/residue: 0.2879
  time to fit residues: 152.3163
Evaluate side-chains
  189 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.183638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.154089 restraints weight = 20048.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.150250 restraints weight = 43841.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.150782 restraints weight = 39414.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10960  Z= 0.158
  Angle     :  0.544   7.205  15036  Z= 0.307
  Chirality :  0.039   0.128   1844
  Planarity :  0.006   0.065   1888
  Dihedral  :  4.270  18.580   1652
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.18 (0.21), residues: 1516
  helix:  1.48 (0.15), residues: 1072
  sheet:  0.09 (0.65), residues: 52
  loop : -0.99 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 167 
 HIS   0.004   0.002   HIS B 161 
 PHE   0.011   0.001   PHE B  21 
 TYR   0.018   0.001   TYR C 272 
 ARG   0.011   0.001   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06121 (  893)
  hydrogen bonds       : angle       4.73936 ( 2595)
  covalent geometry    : bond        0.00307 (10960)
  covalent geometry    : angle       0.54362 (15036)

*********************** 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
  291 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 2.091 
Fit side-chains
REVERT: A   28 PRO cc_start: 0.8959 (Cg_endo) cc_final: 0.8718 (Cg_exo)
REVERT: A  134 GLN cc_start: 0.7921 (tp40) cc_final: 0.7310 (tp-100)
REVERT: A  249 MET cc_start: 0.8823 (ttp) cc_final: 0.8370 (ttm)
REVERT: B  134 GLN cc_start: 0.7876 (tp40) cc_final: 0.7495 (tp40)
REVERT: B  239 ASP cc_start: 0.7977 (t0) cc_final: 0.7776 (t0)
REVERT: B  249 MET cc_start: 0.8881 (ttp) cc_final: 0.8362 (ttm)
REVERT: C  162 TRP cc_start: 0.8546 (m-10) cc_final: 0.8039 (m100)
REVERT: C  249 MET cc_start: 0.8853 (ttp) cc_final: 0.8211 (ttm)
REVERT: D   28 PRO cc_start: 0.8998 (Cg_endo) cc_final: 0.8760 (Cg_exo)
REVERT: D  239 ASP cc_start: 0.8003 (t0) cc_final: 0.7791 (t0)
REVERT: D  249 MET cc_start: 0.8826 (ttp) cc_final: 0.8360 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.3058
  time to fit residues: 123.5822
Evaluate side-chains
  173 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 141 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 135 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 70 optimal weight:   30.0000
   chunk 111 optimal weight:   30.0000
   chunk 81 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.180286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.148590 restraints weight = 21077.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.148442 restraints weight = 46680.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148949 restraints weight = 37319.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10960  Z= 0.151
  Angle     :  0.475   6.679  15036  Z= 0.265
  Chirality :  0.038   0.123   1844
  Planarity :  0.004   0.051   1888
  Dihedral  :  3.772  15.904   1652
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.21), residues: 1516
  helix:  1.78 (0.15), residues: 1084
  sheet:  0.78 (0.79), residues: 48
  loop : -0.61 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  58 
 HIS   0.004   0.002   HIS C 161 
 PHE   0.022   0.002   PHE D 154 
 TYR   0.012   0.001   TYR D 188 
 ARG   0.005   0.001   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05195 (  893)
  hydrogen bonds       : angle       4.18577 ( 2595)
  covalent geometry    : bond        0.00296 (10960)
  covalent geometry    : angle       0.47537 (15036)

*********************** 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
  240 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 2.081 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8888 (ttp) cc_final: 0.8235 (ttm)
REVERT: B  249 MET cc_start: 0.8903 (ttp) cc_final: 0.8231 (ttm)
REVERT: C   10 VAL cc_start: 0.8584 (t) cc_final: 0.8379 (t)
REVERT: C  134 GLN cc_start: 0.7879 (tp40) cc_final: 0.7640 (tp40)
REVERT: C  249 MET cc_start: 0.8966 (ttp) cc_final: 0.8337 (ttm)
REVERT: D  134 GLN cc_start: 0.7877 (tp40) cc_final: 0.7325 (tp-100)
REVERT: D  249 MET cc_start: 0.8871 (ttp) cc_final: 0.8192 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2603
  time to fit residues: 88.9903
Evaluate side-chains
  172 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   chunk 55 optimal weight:    0.5980
   chunk 113 optimal weight:    9.9990
   chunk 135 optimal weight:    4.9990
   chunk 144 optimal weight:    0.9990
   chunk 118 optimal weight:    9.9990
   chunk 94 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 106 optimal weight:   50.0000
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
D 141 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.181267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.151264 restraints weight = 20508.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.149316 restraints weight = 54579.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.149697 restraints weight = 48244.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.5149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10960  Z= 0.122
  Angle     :  0.457   6.567  15036  Z= 0.250
  Chirality :  0.037   0.121   1844
  Planarity :  0.003   0.043   1888
  Dihedral  :  3.605  14.070   1652
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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:  2.07 (0.21), residues: 1516
  helix:  2.00 (0.15), residues: 1096
  sheet: -0.65 (0.55), residues: 88
  loop : -0.08 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  58 
 HIS   0.002   0.001   HIS A 161 
 PHE   0.016   0.001   PHE D 154 
 TYR   0.012   0.001   TYR B 273 
 ARG   0.004   0.000   ARG B 135 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  893)
  hydrogen bonds       : angle       3.91179 ( 2595)
  covalent geometry    : bond        0.00237 (10960)
  covalent geometry    : angle       0.45709 (15036)

*********************** 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
  228 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.7617 (tp40) cc_final: 0.7379 (tp40)
REVERT: B  134 GLN cc_start: 0.7288 (tp40) cc_final: 0.6997 (tp40)
REVERT: B  249 MET cc_start: 0.8746 (ttp) cc_final: 0.8236 (ttm)
REVERT: C   54 LEU cc_start: 0.8921 (mt) cc_final: 0.8591 (mt)
REVERT: C  249 MET cc_start: 0.8798 (ttp) cc_final: 0.8295 (ttm)
REVERT: D   10 VAL cc_start: 0.8400 (t) cc_final: 0.8188 (t)
REVERT: D  249 MET cc_start: 0.8686 (ttp) cc_final: 0.8097 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2325
  time to fit residues: 76.2230
Evaluate side-chains
  170 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 136 optimal weight:    3.9990
   chunk 123 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 114 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
B 141 GLN
C 134 GLN
C 141 GLN
D 134 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.181836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.160652 restraints weight = 20287.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.159170 restraints weight = 51048.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.159058 restraints weight = 49120.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10960  Z= 0.119
  Angle     :  0.448   6.584  15036  Z= 0.243
  Chirality :  0.037   0.121   1844
  Planarity :  0.003   0.040   1888
  Dihedral  :  3.421  14.145   1652
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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:  2.69 (0.21), residues: 1516
  helix:  2.52 (0.15), residues: 1068
  sheet: -0.45 (0.57), residues: 88
  loop :  0.15 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  58 
 HIS   0.003   0.002   HIS C 161 
 PHE   0.025   0.002   PHE A 154 
 TYR   0.012   0.001   TYR C 188 
 ARG   0.002   0.000   ARG B   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  893)
  hydrogen bonds       : angle       3.72616 ( 2595)
  covalent geometry    : bond        0.00234 (10960)
  covalent geometry    : angle       0.44791 (15036)

*********************** 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
  221 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8852 (mt) cc_final: 0.8392 (mt)
REVERT: A  165 VAL cc_start: 0.9290 (t) cc_final: 0.9022 (p)
REVERT: B   10 VAL cc_start: 0.8415 (t) cc_final: 0.8179 (t)
REVERT: B   54 LEU cc_start: 0.8883 (mt) cc_final: 0.8580 (tp)
REVERT: B   56 ILE cc_start: 0.7952 (mm) cc_final: 0.7691 (mm)
REVERT: B  165 VAL cc_start: 0.9292 (t) cc_final: 0.9036 (p)
REVERT: B  249 MET cc_start: 0.8666 (ttp) cc_final: 0.8174 (ttm)
REVERT: C   10 VAL cc_start: 0.8438 (t) cc_final: 0.8227 (t)
REVERT: C   56 ILE cc_start: 0.8003 (mm) cc_final: 0.7761 (mm)
REVERT: C  134 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7497 (tp-100)
REVERT: C  165 VAL cc_start: 0.9292 (t) cc_final: 0.9038 (p)
REVERT: C  249 MET cc_start: 0.8688 (ttp) cc_final: 0.8157 (ttm)
REVERT: D   10 VAL cc_start: 0.8434 (t) cc_final: 0.8222 (t)
REVERT: D   56 ILE cc_start: 0.8012 (mm) cc_final: 0.7782 (mm)
REVERT: D  134 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7534 (tp-100)
REVERT: D  165 VAL cc_start: 0.9288 (t) cc_final: 0.9026 (p)
REVERT: D  249 MET cc_start: 0.8610 (ttp) cc_final: 0.8077 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2021
  time to fit residues: 65.6867
Evaluate side-chains
  180 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 91 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 125 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 70 optimal weight:   50.0000
   overall best weight:    1.3400

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.179924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151549 restraints weight = 20188.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.151347 restraints weight = 50440.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.151447 restraints weight = 40408.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.5909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10960  Z= 0.155
  Angle     :  0.499   6.615  15036  Z= 0.264
  Chirality :  0.037   0.121   1844
  Planarity :  0.003   0.039   1888
  Dihedral  :  3.409  13.995   1652
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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:  2.64 (0.21), residues: 1516
  helix:  2.54 (0.14), residues: 1064
  sheet: -0.45 (0.56), residues: 88
  loop : -0.08 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  12 
 HIS   0.004   0.002   HIS D 161 
 PHE   0.024   0.002   PHE D 154 
 TYR   0.014   0.001   TYR D 188 
 ARG   0.004   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04907 (  893)
  hydrogen bonds       : angle       3.82226 ( 2595)
  covalent geometry    : bond        0.00340 (10960)
  covalent geometry    : angle       0.49885 (15036)

*********************** 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
  187 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7100 (tp40)
REVERT: A  165 VAL cc_start: 0.9309 (t) cc_final: 0.9059 (p)
REVERT: A  230 ASN cc_start: 0.9221 (t0) cc_final: 0.8928 (t0)
REVERT: B    7 ARG cc_start: 0.3934 (mtp180) cc_final: 0.3137 (ttm110)
REVERT: B   10 VAL cc_start: 0.8200 (t) cc_final: 0.7976 (t)
REVERT: B   89 ASP cc_start: 0.7228 (t70) cc_final: 0.6551 (t0)
REVERT: B  134 GLN cc_start: 0.7307 (tp-100) cc_final: 0.7083 (tp40)
REVERT: B  230 ASN cc_start: 0.9228 (t0) cc_final: 0.8920 (t0)
REVERT: C   10 VAL cc_start: 0.8316 (t) cc_final: 0.8085 (t)
REVERT: C  134 GLN cc_start: 0.7249 (tp-100) cc_final: 0.6791 (tp-100)
REVERT: C  230 ASN cc_start: 0.9187 (t0) cc_final: 0.8892 (t0)
REVERT: D   10 VAL cc_start: 0.8342 (t) cc_final: 0.8108 (t)
REVERT: D  134 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6821 (tp-100)
REVERT: D  230 ASN cc_start: 0.9200 (t0) cc_final: 0.8911 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1963
  time to fit residues: 53.8719
Evaluate side-chains
  142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0670
   chunk 107 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   chunk 114 optimal weight:    6.9990
   chunk 124 optimal weight:    0.4980
   chunk 33 optimal weight:   30.0000
   chunk 94 optimal weight:    0.5980
   chunk 102 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   overall best weight:    2.2322

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.174599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141602 restraints weight = 21081.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138321 restraints weight = 31171.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.134868 restraints weight = 30007.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
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      :  0.005   0.039  10960  Z= 0.224
  Angle     :  0.604   7.114  15036  Z= 0.319
  Chirality :  0.039   0.123   1844
  Planarity :  0.003   0.036   1888
  Dihedral  :  3.702  14.009   1652
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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:  2.22 (0.21), residues: 1516
  helix:  2.34 (0.15), residues: 1060
  sheet: -0.78 (0.56), residues: 88
  loop : -0.56 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 155 
 HIS   0.005   0.003   HIS A 161 
 PHE   0.023   0.003   PHE B  47 
 TYR   0.029   0.002   TYR A  45 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05889 (  893)
  hydrogen bonds       : angle       4.23298 ( 2595)
  covalent geometry    : bond        0.00509 (10960)
  covalent geometry    : angle       0.60417 (15036)

*********************** 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
  188 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.8009 (mm) cc_final: 0.7616 (pt)
REVERT: A  134 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7489 (tp40)
REVERT: A  138 LEU cc_start: 0.8853 (pp) cc_final: 0.8639 (pp)
REVERT: A  230 ASN cc_start: 0.9225 (t0) cc_final: 0.8977 (t0)
REVERT: B    7 ARG cc_start: 0.4322 (mtp180) cc_final: 0.3642 (ttm110)
REVERT: B  134 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7431 (tp40)
REVERT: B  138 LEU cc_start: 0.9029 (pp) cc_final: 0.8815 (pp)
REVERT: B  230 ASN cc_start: 0.9233 (t0) cc_final: 0.8941 (t0)
REVERT: C  134 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7248 (tp-100)
REVERT: C  165 VAL cc_start: 0.9487 (t) cc_final: 0.9252 (p)
REVERT: C  230 ASN cc_start: 0.9236 (t0) cc_final: 0.8971 (t0)
REVERT: D   97 GLU cc_start: 0.7446 (pm20) cc_final: 0.7115 (mm-30)
REVERT: D  134 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7230 (tp-100)
REVERT: D  230 ASN cc_start: 0.9249 (t0) cc_final: 0.9007 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2692
  time to fit residues: 73.3329
Evaluate side-chains
  150 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9980
   chunk 33 optimal weight:   40.0000
   chunk 60 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0670
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.7318

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.178451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.139779 restraints weight = 20944.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.133127 restraints weight = 25032.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.128817 restraints weight = 21127.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.6423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10960  Z= 0.119
  Angle     :  0.460   6.932  15036  Z= 0.243
  Chirality :  0.037   0.120   1844
  Planarity :  0.003   0.034   1888
  Dihedral  :  3.346  13.042   1652
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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:  2.71 (0.21), residues: 1516
  helix:  2.69 (0.14), residues: 1068
  sheet: -0.55 (0.58), residues: 88
  loop : -0.41 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  85 
 HIS   0.001   0.001   HIS A 161 
 PHE   0.022   0.002   PHE D 154 
 TYR   0.015   0.001   TYR C  45 
 ARG   0.005   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04656 (  893)
  hydrogen bonds       : angle       3.80642 ( 2595)
  covalent geometry    : bond        0.00237 (10960)
  covalent geometry    : angle       0.46008 (15036)

*********************** 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
  217 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.7993 (mm) cc_final: 0.7605 (pt)
REVERT: A  134 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7850 (tp-100)
REVERT: A  230 ASN cc_start: 0.9012 (t0) cc_final: 0.8722 (t0)
REVERT: B    7 ARG cc_start: 0.4048 (mtp180) cc_final: 0.3634 (ttm110)
REVERT: B  134 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7814 (tp40)
REVERT: B  230 ASN cc_start: 0.9016 (t0) cc_final: 0.8747 (t0)
REVERT: C  134 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7429 (tp-100)
REVERT: C  230 ASN cc_start: 0.9041 (t0) cc_final: 0.8807 (t0)
REVERT: D  134 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7394 (tp-100)
REVERT: D  230 ASN cc_start: 0.9051 (t0) cc_final: 0.8820 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2549
  time to fit residues: 77.4511
Evaluate side-chains
  157 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 103 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0470
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 97 optimal weight:    0.1980
   chunk 76 optimal weight:    8.9990
   overall best weight:    0.5078

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.179629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.136589 restraints weight = 21394.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.123466 restraints weight = 27871.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124476 restraints weight = 21563.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.6633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10960  Z= 0.110
  Angle     :  0.468   7.537  15036  Z= 0.241
  Chirality :  0.036   0.124   1844
  Planarity :  0.003   0.033   1888
  Dihedral  :  3.229  12.745   1652
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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:  2.85 (0.21), residues: 1516
  helix:  2.79 (0.15), residues: 1068
  sheet: -0.42 (0.58), residues: 88
  loop : -0.34 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  12 
 HIS   0.001   0.001   HIS C 161 
 PHE   0.028   0.001   PHE B 154 
 TYR   0.008   0.001   TYR B 169 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  893)
  hydrogen bonds       : angle       3.65342 ( 2595)
  covalent geometry    : bond        0.00212 (10960)
  covalent geometry    : angle       0.46763 (15036)

*********************** 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
  217 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 TRP cc_start: 0.8390 (t-100) cc_final: 0.8102 (t-100)
REVERT: A   89 ASP cc_start: 0.7573 (m-30) cc_final: 0.7201 (m-30)
REVERT: A   97 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6912 (tp30)
REVERT: A  134 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8147 (tp40)
REVERT: A  230 ASN cc_start: 0.9116 (t0) cc_final: 0.8838 (t0)
REVERT: B    7 ARG cc_start: 0.3839 (mtp180) cc_final: 0.3492 (ttm110)
REVERT: B   45 TYR cc_start: 0.7821 (m-80) cc_final: 0.7479 (m-80)
REVERT: B  134 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7986 (tp40)
REVERT: B  171 ASP cc_start: 0.7570 (m-30) cc_final: 0.7212 (t0)
REVERT: B  230 ASN cc_start: 0.9042 (t0) cc_final: 0.8802 (t0)
REVERT: B  249 MET cc_start: 0.7923 (ttm) cc_final: 0.7711 (ttm)
REVERT: B  271 ASP cc_start: 0.8274 (m-30) cc_final: 0.8070 (m-30)
REVERT: C    7 ARG cc_start: 0.3799 (mtp180) cc_final: 0.3388 (ttm170)
REVERT: C   89 ASP cc_start: 0.8538 (t0) cc_final: 0.8242 (m-30)
REVERT: C  134 GLN cc_start: 0.8464 (tp-100) cc_final: 0.7878 (tp40)
REVERT: C  230 ASN cc_start: 0.9133 (t0) cc_final: 0.8878 (t0)
REVERT: D    7 ARG cc_start: 0.3668 (mtp180) cc_final: 0.3221 (ttm170)
REVERT: D   89 ASP cc_start: 0.8585 (t0) cc_final: 0.7837 (m-30)
REVERT: D  134 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7684 (tp-100)
REVERT: D  171 ASP cc_start: 0.7739 (m-30) cc_final: 0.7359 (t0)
REVERT: D  230 ASN cc_start: 0.9011 (t0) cc_final: 0.8793 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.3070
  time to fit residues: 94.2038
Evaluate side-chains
  175 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0980
   chunk 55 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.179787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.145469 restraints weight = 21444.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.142675 restraints weight = 29394.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139074 restraints weight = 29340.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.6778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10960  Z= 0.110
  Angle     :  0.460   8.994  15036  Z= 0.238
  Chirality :  0.036   0.119   1844
  Planarity :  0.003   0.033   1888
  Dihedral  :  3.183  12.564   1652
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  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:  2.90 (0.21), residues: 1516
  helix:  2.83 (0.14), residues: 1068
  sheet: -0.50 (0.56), residues: 88
  loop : -0.30 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  22 
 HIS   0.002   0.001   HIS C 161 
 PHE   0.027   0.002   PHE B 154 
 TYR   0.008   0.001   TYR C 188 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (  893)
  hydrogen bonds       : angle       3.60860 ( 2595)
  covalent geometry    : bond        0.00219 (10960)
  covalent geometry    : angle       0.46043 (15036)

********************** 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
  224 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.138 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6712 (tp30)
REVERT: A  134 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7891 (tp40)
REVERT: A  230 ASN cc_start: 0.9185 (t0) cc_final: 0.8952 (t0)
REVERT: A  249 MET cc_start: 0.8029 (tpp) cc_final: 0.7399 (ttm)
REVERT: B    7 ARG cc_start: 0.3993 (mtp180) cc_final: 0.3643 (ttm110)
REVERT: B  134 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7805 (tp40)
REVERT: B  171 ASP cc_start: 0.7471 (m-30) cc_final: 0.7194 (t0)
REVERT: B  230 ASN cc_start: 0.9201 (t0) cc_final: 0.8966 (t0)
REVERT: C    7 ARG cc_start: 0.3980 (mtp180) cc_final: 0.3552 (ttm170)
REVERT: C   56 ILE cc_start: 0.7696 (mm) cc_final: 0.7465 (mm)
REVERT: C  134 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7458 (tp40)
REVERT: C  171 ASP cc_start: 0.7296 (m-30) cc_final: 0.6910 (t0)
REVERT: C  230 ASN cc_start: 0.9188 (t0) cc_final: 0.8946 (t0)
REVERT: C  274 MET cc_start: 0.8168 (mmm) cc_final: 0.7960 (mmm)
REVERT: D    7 ARG cc_start: 0.3974 (mtp180) cc_final: 0.3603 (ttm170)
REVERT: D   52 PHE cc_start: 0.8237 (m-10) cc_final: 0.8022 (m-80)
REVERT: D  134 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7418 (tp40)
REVERT: D  171 ASP cc_start: 0.7499 (m-30) cc_final: 0.7209 (t0)
REVERT: D  230 ASN cc_start: 0.9163 (t0) cc_final: 0.8922 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2068
  time to fit residues: 67.4095
Evaluate side-chains
  177 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 146 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 111 optimal weight:   40.0000
   chunk 113 optimal weight:   40.0000
   chunk 22 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 137 optimal weight:    0.1980
   chunk 144 optimal weight:   40.0000
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.175662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136685 restraints weight = 20940.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 114)---------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118160 restraints weight = 33617.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117688 restraints weight = 27070.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.6828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10960  Z= 0.206
  Angle     :  0.591   9.074  15036  Z= 0.310
  Chirality :  0.039   0.119   1844
  Planarity :  0.003   0.034   1888
  Dihedral  :  3.509  14.430   1652
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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:  2.38 (0.21), residues: 1516
  helix:  2.46 (0.15), residues: 1064
  sheet: -0.65 (0.56), residues: 88
  loop : -0.53 (0.36), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  22 
 HIS   0.005   0.003   HIS B 161 
 PHE   0.023   0.003   PHE B 154 
 TYR   0.015   0.002   TYR D 188 
 ARG   0.003   0.000   ARG B 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05478 (  893)
  hydrogen bonds       : angle       4.08926 ( 2595)
  covalent geometry    : bond        0.00471 (10960)
  covalent geometry    : angle       0.59057 (15036)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3504.28 seconds
wall clock time: 64 minutes 40.85 seconds (3880.85 seconds total)