Starting phenix.real_space_refine
on Tue Nov 18 03:53:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5v4s_8632/11_2025/5v4s_8632.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5v4s_8632/11_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_8632/11_2025/5v4s_8632.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5v4s_8632/11_2025/5v4s_8632.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5v4s_8632/11_2025/5v4s_8632.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5v4s_8632/11_2025/5v4s_8632.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'GLU:plan': 13, 'ASP:plan': 13, 'ASN:plan1': 3, 'ARG:plan': 9, 'GLN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 9, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 239
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.14, per 1000 atoms: 0.20
  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: 1.10
  Conformation dependent library (CDL) restraints added in 431.6 milliseconds
  

  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: 0.38
  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: 1.99

  Time building geometry restraints manager: 1.42 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             0.800
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.120
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.610
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.001   ARG C  30 
 TYR   0.034   0.005   TYR A 272 
 PHE   0.011   0.002   PHE D  21 
 TRP   0.022   0.003   TRP C  58 
 HIS   0.002   0.002   HIS D 161 

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

*********************** 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  : 0.402 
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: 0.1279
  time to fit residues: 67.7878
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  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    0.0170
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.3822

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.181202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.156777 restraints weight = 20685.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.153715 restraints weight = 40362.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.148224 restraints weight = 39622.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.147934 restraints weight = 48681.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.147294 restraints weight = 35444.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10960  Z= 0.185
  Angle     :  0.572   7.315  15036  Z= 0.322
  Chirality :  0.039   0.140   1844
  Planarity :  0.006   0.066   1888
  Dihedral  :  4.303  18.879   1652
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.21), residues: 1516
  helix:  1.33 (0.15), residues: 1072
  sheet:  0.12 (0.68), residues: 52
  loop : -1.05 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A   9 
 TYR   0.020   0.002   TYR C 272 
 PHE   0.014   0.001   PHE C  21 
 TRP   0.017   0.002   TRP A  85 
 HIS   0.004   0.003   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10960)
  covalent geometry    : angle       0.57229 (15036)
  hydrogen bonds       : bond        0.06262 (  893)
  hydrogen bonds       : angle       4.81634 ( 2595)

*********************** 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
  272 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.7940 (tp40) cc_final: 0.7573 (tp40)
REVERT: A  249 MET cc_start: 0.8938 (ttp) cc_final: 0.8448 (ttm)
REVERT: B  134 GLN cc_start: 0.7911 (tp40) cc_final: 0.7589 (tp40)
REVERT: B  249 MET cc_start: 0.8940 (ttp) cc_final: 0.8388 (ttm)
REVERT: C  249 MET cc_start: 0.9053 (ttp) cc_final: 0.8329 (ttm)
REVERT: D    7 ARG cc_start: 0.3729 (mtp180) cc_final: 0.3186 (ttm110)
REVERT: D  249 MET cc_start: 0.8903 (ttp) cc_final: 0.8380 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1155
  time to fit residues: 42.9679
Evaluate side-chains
  155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0070
   chunk 141 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 113 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5798

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.185535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.146532 restraints weight = 20500.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.142752 restraints weight = 38264.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.143475 restraints weight = 33855.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.143691 restraints weight = 21446.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.143936 restraints weight = 21873.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10960  Z= 0.125
  Angle     :  0.462   6.648  15036  Z= 0.256
  Chirality :  0.037   0.122   1844
  Planarity :  0.004   0.060   1888
  Dihedral  :  3.704  14.793   1652
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.21), residues: 1516
  helix:  1.92 (0.15), residues: 1084
  sheet:  0.72 (0.79), residues: 48
  loop : -0.65 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   9 
 TYR   0.008   0.001   TYR D 188 
 PHE   0.023   0.001   PHE A 154 
 TRP   0.008   0.001   TRP C 189 
 HIS   0.002   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10960)
  covalent geometry    : angle       0.46192 (15036)
  hydrogen bonds       : bond        0.04880 (  893)
  hydrogen bonds       : angle       4.09726 ( 2595)

*********************** 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
  247 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  194 ILE cc_start: 0.8608 (mt) cc_final: 0.8383 (mt)
REVERT: A  249 MET cc_start: 0.8868 (ttp) cc_final: 0.8180 (ttm)
REVERT: B  138 LEU cc_start: 0.8716 (mt) cc_final: 0.8141 (mt)
REVERT: B  249 MET cc_start: 0.8866 (ttp) cc_final: 0.8175 (ttm)
REVERT: C  134 GLN cc_start: 0.8084 (tp40) cc_final: 0.7751 (tp40)
REVERT: C  162 TRP cc_start: 0.8592 (m-10) cc_final: 0.7992 (m100)
REVERT: C  249 MET cc_start: 0.8821 (ttp) cc_final: 0.8094 (ttm)
REVERT: D    7 ARG cc_start: 0.3584 (mtp180) cc_final: 0.3150 (ttm110)
REVERT: D   58 TRP cc_start: 0.7359 (m100) cc_final: 0.7154 (m100)
REVERT: D  134 GLN cc_start: 0.8074 (tp40) cc_final: 0.7788 (tp40)
REVERT: D  249 MET cc_start: 0.8851 (ttp) cc_final: 0.8146 (ttm)
REVERT: D  274 MET cc_start: 0.8158 (mmm) cc_final: 0.7935 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.0910
  time to fit residues: 33.0821
Evaluate side-chains
  165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 105 optimal weight:   20.0000
   chunk 127 optimal weight:    4.9990
   chunk 40 optimal weight:    0.2980
   chunk 118 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 145 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 114 optimal weight:    7.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.178674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.152894 restraints weight = 20749.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.151317 restraints weight = 50425.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.144016 restraints weight = 32955.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.143345 restraints weight = 42081.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.143174 restraints weight = 31887.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.5160

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= 0.160
  Angle     :  0.515   6.605  15036  Z= 0.278
  Chirality :  0.038   0.122   1844
  Planarity :  0.004   0.047   1888
  Dihedral  :  3.610  15.543   1652
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.21), residues: 1516
  helix:  1.97 (0.15), residues: 1088
  sheet: -0.27 (0.59), residues: 88
  loop : -0.20 (0.37), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 259 
 TYR   0.016   0.002   TYR D 188 
 PHE   0.019   0.002   PHE B 140 
 TRP   0.010   0.001   TRP A  58 
 HIS   0.005   0.003   HIS C 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10960)
  covalent geometry    : angle       0.51497 (15036)
  hydrogen bonds       : bond        0.05294 (  893)
  hydrogen bonds       : angle       4.03267 ( 2595)

*********************** 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
  191 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.3649 (mtp180) cc_final: 0.3336 (ttm110)
REVERT: A   10 VAL cc_start: 0.8446 (t) cc_final: 0.8214 (t)
REVERT: B  134 GLN cc_start: 0.7729 (tm130) cc_final: 0.7329 (tp-100)
REVERT: B  249 MET cc_start: 0.8806 (ttp) cc_final: 0.8193 (ttm)
REVERT: C   10 VAL cc_start: 0.8350 (t) cc_final: 0.8145 (t)
REVERT: C   54 LEU cc_start: 0.8916 (mt) cc_final: 0.8578 (tp)
REVERT: D    7 ARG cc_start: 0.3975 (mtp180) cc_final: 0.3420 (ttm110)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0946
  time to fit residues: 26.1703
Evaluate side-chains
  147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 113 optimal weight:   50.0000
   chunk 38 optimal weight:    8.9990
   chunk 149 optimal weight:   40.0000
   chunk 67 optimal weight:   40.0000
   chunk 124 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.9986

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.175462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.146089 restraints weight = 20675.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143676 restraints weight = 56185.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.144170 restraints weight = 48295.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145992 restraints weight = 30214.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145070 restraints weight = 27617.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  10960  Z= 0.204
  Angle     :  0.572   7.080  15036  Z= 0.308
  Chirality :  0.039   0.128   1844
  Planarity :  0.004   0.050   1888
  Dihedral  :  3.701  14.679   1652
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.21), residues: 1516
  helix:  1.97 (0.15), residues: 1084
  sheet: -0.44 (0.60), residues: 88
  loop : -0.46 (0.36), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 268 
 TYR   0.017   0.002   TYR D 188 
 PHE   0.023   0.003   PHE B 154 
 TRP   0.010   0.001   TRP C 155 
 HIS   0.005   0.003   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (10960)
  covalent geometry    : angle       0.57204 (15036)
  hydrogen bonds       : bond        0.05815 (  893)
  hydrogen bonds       : angle       4.23692 ( 2595)

*********************** 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
  186 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ILE cc_start: 0.8277 (mm) cc_final: 0.8008 (mm)
REVERT: A  134 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7620 (tp-100)
REVERT: B  134 GLN cc_start: 0.7810 (tm130) cc_final: 0.7296 (tp-100)
REVERT: B  249 MET cc_start: 0.8780 (ttp) cc_final: 0.8273 (ttm)
REVERT: C  134 GLN cc_start: 0.7685 (tp-100) cc_final: 0.6912 (tp40)
REVERT: D    7 ARG cc_start: 0.4143 (mtp180) cc_final: 0.3695 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1046
  time to fit residues: 27.3491
Evaluate side-chains
  147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 145 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 109 optimal weight:   40.0000
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
C 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.177215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151902 restraints weight = 20841.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.149851 restraints weight = 51540.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.149235 restraints weight = 37773.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.147634 restraints weight = 32601.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.147784 restraints weight = 27143.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.6024

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= 0.154
  Angle     :  0.497   7.038  15036  Z= 0.269
  Chirality :  0.037   0.122   1844
  Planarity :  0.003   0.043   1888
  Dihedral  :  3.532  14.506   1652
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.29 (0.21), residues: 1516
  helix:  2.28 (0.14), residues: 1088
  sheet: -0.47 (0.59), residues: 88
  loop : -0.45 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.011   0.001   TYR D 188 
 PHE   0.022   0.002   PHE B 154 
 TRP   0.013   0.001   TRP D  85 
 HIS   0.003   0.002   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10960)
  covalent geometry    : angle       0.49670 (15036)
  hydrogen bonds       : bond        0.05221 (  893)
  hydrogen bonds       : angle       4.02474 ( 2595)

*********************** 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
  198 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7205 (tp40)
REVERT: A  165 VAL cc_start: 0.9362 (t) cc_final: 0.9133 (p)
REVERT: B  134 GLN cc_start: 0.7779 (tm130) cc_final: 0.7309 (tp-100)
REVERT: B  165 VAL cc_start: 0.9345 (t) cc_final: 0.9109 (p)
REVERT: B  201 ASP cc_start: 0.8091 (t70) cc_final: 0.7800 (t0)
REVERT: B  249 MET cc_start: 0.8803 (ttp) cc_final: 0.8086 (ttm)
REVERT: C  134 GLN cc_start: 0.7551 (tp-100) cc_final: 0.6607 (tp40)
REVERT: C  274 MET cc_start: 0.8363 (mmm) cc_final: 0.8160 (mmm)
REVERT: D    7 ARG cc_start: 0.4383 (mtp180) cc_final: 0.3908 (ttm110)
REVERT: D  165 VAL cc_start: 0.9344 (t) cc_final: 0.9116 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1026
  time to fit residues: 28.6635
Evaluate side-chains
  151 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 105 optimal weight:   40.0000
   chunk 42 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 117 optimal weight:    3.9990
   chunk 132 optimal weight:    0.6980
   chunk 126 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 134 GLN
C 141 GLN
D 141 GLN
D 245 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.179009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.150184 restraints weight = 20585.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.148699 restraints weight = 46727.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149291 restraints weight = 39066.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.148204 restraints weight = 31312.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.148541 restraints weight = 28984.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.6317

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= 0.130
  Angle     :  0.480   6.838  15036  Z= 0.257
  Chirality :  0.037   0.122   1844
  Planarity :  0.003   0.040   1888
  Dihedral  :  3.435  14.133   1652
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.21), residues: 1516
  helix:  2.65 (0.14), residues: 1064
  sheet: -0.32 (0.61), residues: 88
  loop : -0.31 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 270 
 TYR   0.010   0.001   TYR D 188 
 PHE   0.021   0.001   PHE B 154 
 TRP   0.017   0.001   TRP B  85 
 HIS   0.002   0.001   HIS C 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10960)
  covalent geometry    : angle       0.48047 (15036)
  hydrogen bonds       : bond        0.04718 (  893)
  hydrogen bonds       : angle       3.86709 ( 2595)

*********************** 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
  200 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 VAL cc_start: 0.9341 (t) cc_final: 0.9113 (p)
REVERT: B   10 VAL cc_start: 0.8134 (t) cc_final: 0.7912 (t)
REVERT: C   97 GLU cc_start: 0.7200 (pm20) cc_final: 0.6875 (mm-30)
REVERT: C  134 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7180 (tp40)
REVERT: D    7 ARG cc_start: 0.4319 (mtp180) cc_final: 0.3732 (ttm110)
REVERT: D  165 VAL cc_start: 0.9316 (t) cc_final: 0.9103 (p)
REVERT: D  265 ILE cc_start: 0.8040 (mp) cc_final: 0.7715 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0976
  time to fit residues: 28.0950
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  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 3 optimal weight:    3.9990
   chunk 146 optimal weight:   40.0000
   chunk 9 optimal weight:    1.9990
   chunk 135 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 66 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:   20.0000
   chunk 150 optimal weight:   40.0000
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.174623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145185 restraints weight = 21571.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143267 restraints weight = 31807.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140823 restraints weight = 29277.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.139718 restraints weight = 30482.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.138769 restraints weight = 28002.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.6544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10960  Z= 0.174
  Angle     :  0.536   7.389  15036  Z= 0.285
  Chirality :  0.038   0.138   1844
  Planarity :  0.003   0.043   1888
  Dihedral  :  3.524  14.772   1652
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.21), residues: 1516
  helix:  2.46 (0.14), residues: 1068
  sheet: -0.34 (0.62), residues: 88
  loop : -0.43 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.013   0.002   TYR B 188 
 PHE   0.020   0.002   PHE B 154 
 TRP   0.016   0.001   TRP D  58 
 HIS   0.004   0.002   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10960)
  covalent geometry    : angle       0.53617 (15036)
  hydrogen bonds       : bond        0.05279 (  893)
  hydrogen bonds       : angle       4.07064 ( 2595)

*********************** 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
  188 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LYS cc_start: 0.8221 (tmmt) cc_final: 0.7638 (tmmt)
REVERT: B   97 GLU cc_start: 0.7353 (pm20) cc_final: 0.6919 (mm-30)
REVERT: B  134 GLN cc_start: 0.8265 (tm130) cc_final: 0.8017 (tm-30)
REVERT: C   41 LEU cc_start: 0.8221 (mm) cc_final: 0.7748 (pt)
REVERT: C   97 GLU cc_start: 0.7483 (pm20) cc_final: 0.6953 (mm-30)
REVERT: C  134 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7718 (tp40)
REVERT: C  138 LEU cc_start: 0.8796 (mt) cc_final: 0.8445 (mt)
REVERT: D    7 ARG cc_start: 0.4397 (mtp180) cc_final: 0.3811 (ttm110)
REVERT: D   97 GLU cc_start: 0.7431 (pm20) cc_final: 0.7228 (tp30)
REVERT: D  134 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7168 (tp40)
REVERT: D  138 LEU cc_start: 0.8823 (pp) cc_final: 0.8528 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1002
  time to fit residues: 27.1986
Evaluate side-chains
  152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 50 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 135 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 104 optimal weight:   10.0000
   chunk 128 optimal weight:    0.8980
   chunk 70 optimal weight:   50.0000
   chunk 99 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 245 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.178035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115603 restraints weight = 22115.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116737 restraints weight = 14526.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117491 restraints weight = 11750.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117478 restraints weight = 9617.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117609 restraints weight = 10051.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.6762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10960  Z= 0.119
  Angle     :  0.481   8.122  15036  Z= 0.253
  Chirality :  0.037   0.123   1844
  Planarity :  0.003   0.040   1888
  Dihedral  :  3.346  13.694   1652
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.22), residues: 1516
  helix:  2.73 (0.14), residues: 1068
  sheet: -0.19 (0.63), residues: 88
  loop : -0.35 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.011   0.001   TYR A  98 
 PHE   0.021   0.001   PHE A 154 
 TRP   0.017   0.001   TRP A  12 
 HIS   0.001   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10960)
  covalent geometry    : angle       0.48092 (15036)
  hydrogen bonds       : bond        0.04471 (  893)
  hydrogen bonds       : angle       3.84089 ( 2595)

*********************** 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
  209 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7785 (tmmt)
REVERT: B   97 GLU cc_start: 0.7334 (pm20) cc_final: 0.7054 (tp30)
REVERT: B  134 GLN cc_start: 0.8644 (tm130) cc_final: 0.8187 (tm-30)
REVERT: B  138 LEU cc_start: 0.8316 (mt) cc_final: 0.8080 (mt)
REVERT: B  271 ASP cc_start: 0.8385 (m-30) cc_final: 0.8183 (m-30)
REVERT: C   97 GLU cc_start: 0.7542 (pm20) cc_final: 0.6861 (mm-30)
REVERT: C  134 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8328 (tm-30)
REVERT: D    7 ARG cc_start: 0.4004 (mtp180) cc_final: 0.3603 (ttm110)
REVERT: D   22 TRP cc_start: 0.8430 (t-100) cc_final: 0.8107 (t-100)
REVERT: D   89 ASP cc_start: 0.8423 (t0) cc_final: 0.8013 (m-30)
REVERT: D   97 GLU cc_start: 0.7388 (pm20) cc_final: 0.7086 (tp30)
REVERT: D  134 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7466 (tp40)
REVERT: D  138 LEU cc_start: 0.8992 (pp) cc_final: 0.8707 (pp)
REVERT: D  265 ILE cc_start: 0.8844 (mp) cc_final: 0.8511 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1008
  time to fit residues: 30.1313
Evaluate side-chains
  161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 129 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 138 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.178616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.136646 restraints weight = 22108.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 134)---------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116702 restraints weight = 29230.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.116793 restraints weight = 19312.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117989 restraints weight = 14547.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118832 restraints weight = 12209.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.6895

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= 0.124
  Angle     :  0.501   8.708  15036  Z= 0.260
  Chirality :  0.037   0.137   1844
  Planarity :  0.003   0.037   1888
  Dihedral  :  3.293  13.478   1652
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.99
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.22), residues: 1516
  helix:  2.67 (0.14), residues: 1068
  sheet: -0.20 (0.62), residues: 88
  loop : -0.23 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 270 
 TYR   0.013   0.001   TYR A  98 
 PHE   0.035   0.001   PHE B 154 
 TRP   0.014   0.001   TRP C  22 
 HIS   0.002   0.001   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10960)
  covalent geometry    : angle       0.50131 (15036)
  hydrogen bonds       : bond        0.04476 (  893)
  hydrogen bonds       : angle       3.83538 ( 2595)

********************** 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
  208 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 ARG cc_start: 0.3261 (mtp180) cc_final: 0.3058 (ttm-80)
REVERT: A  253 ASP cc_start: 0.8325 (m-30) cc_final: 0.7983 (m-30)
REVERT: B   97 GLU cc_start: 0.7383 (pm20) cc_final: 0.6866 (mm-30)
REVERT: B  134 GLN cc_start: 0.8654 (tm130) cc_final: 0.8254 (tm-30)
REVERT: B  171 ASP cc_start: 0.7623 (m-30) cc_final: 0.7307 (t0)
REVERT: B  201 ASP cc_start: 0.8023 (t70) cc_final: 0.7788 (t0)
REVERT: B  253 ASP cc_start: 0.8453 (m-30) cc_final: 0.8030 (m-30)
REVERT: C    7 ARG cc_start: 0.3869 (mtp180) cc_final: 0.3402 (ttm170)
REVERT: C   97 GLU cc_start: 0.7538 (pm20) cc_final: 0.6863 (mm-30)
REVERT: C  138 LEU cc_start: 0.8850 (mt) cc_final: 0.8529 (pp)
REVERT: D    7 ARG cc_start: 0.3857 (mtp180) cc_final: 0.3428 (ttm110)
REVERT: D   97 GLU cc_start: 0.7381 (pm20) cc_final: 0.7077 (tp30)
REVERT: D  118 LEU cc_start: 0.8553 (mp) cc_final: 0.8327 (mp)
REVERT: D  134 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7314 (tp40)
REVERT: D  138 LEU cc_start: 0.8965 (pp) cc_final: 0.8667 (pp)
REVERT: D  248 LYS cc_start: 0.8078 (tmmt) cc_final: 0.7764 (tmmt)
REVERT: D  265 ILE cc_start: 0.8784 (mp) cc_final: 0.8439 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0908
  time to fit residues: 27.7756
Evaluate side-chains
  166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:   40.0000
   chunk 82 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 105 optimal weight:   40.0000
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
B 134 GLN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.178163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.137623 restraints weight = 22123.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.121543 restraints weight = 31478.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120579 restraints weight = 30691.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120623 restraints weight = 25986.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120604 restraints weight = 22229.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.7029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10960  Z= 0.119
  Angle     :  0.490   8.052  15036  Z= 0.254
  Chirality :  0.037   0.133   1844
  Planarity :  0.003   0.038   1888
  Dihedral  :  3.248  13.127   1652
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.22), residues: 1516
  helix:  2.72 (0.14), residues: 1068
  sheet: -0.18 (0.61), residues: 88
  loop : -0.22 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 270 
 TYR   0.015   0.001   TYR A  98 
 PHE   0.021   0.001   PHE B 154 
 TRP   0.023   0.001   TRP B  12 
 HIS   0.002   0.001   HIS D 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10960)
  covalent geometry    : angle       0.48977 (15036)
  hydrogen bonds       : bond        0.04390 (  893)
  hydrogen bonds       : angle       3.82288 ( 2595)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1673.78 seconds
wall clock time: 29 minutes 35.59 seconds (1775.59 seconds total)