Starting phenix.real_space_refine
on Fri Feb 14 23:28:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5v4s_8632/02_2025/5v4s_8632.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5v4s_8632/02_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_8632/02_2025/5v4s_8632.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5v4s_8632/02_2025/5v4s_8632.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5v4s_8632/02_2025/5v4s_8632.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5v4s_8632/02_2025/5v4s_8632.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    6992      2.51       5
     N    1844      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10756
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 2689
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 132}
          Link IDs: {'PTRANS': 10, 'TRANS': 376}
          Chain breaks: 3
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 456
          Unresolved non-hydrogen angles: 579
          Unresolved non-hydrogen dihedrals: 366
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 239
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 4.80, per 1000 atoms: 0.45
  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: 2.88
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 8 sheets defined
      74.2% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 27
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE A  31 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 59
    Processing helix  chain 'A' and resid 84 through 93
    Processing helix  chain 'A' and resid 95 through 104
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU A 124 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LYS A 125 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 141
      removed outlier: 4.024A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
    Processing helix  chain 'A' and resid 179 through 195
    Processing helix  chain 'A' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 290
    Processing helix  chain 'A' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU A 310 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 319 through 330
    Processing helix  chain 'A' and resid 380 through 386
    Processing helix  chain 'A' and resid 407 through 417
    Processing helix  chain 'A' and resid 417 through 429
      removed outlier: 3.884A  pdb=" N   ILE A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 429 " --> pdb=" O   GLU A 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 27
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE B  31 " --> pdb=" O   PRO B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 59
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 95 through 104
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU B 124 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS B 125 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 173
    Processing helix  chain 'B' and resid 179 through 195
    Processing helix  chain 'B' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET B 249 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG B 268 " --> pdb=" O   ASN B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 290
    Processing helix  chain 'B' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B 310 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 319 through 330
    Processing helix  chain 'B' and resid 380 through 386
    Processing helix  chain 'B' and resid 407 through 417
    Processing helix  chain 'B' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER B 427 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA B 429 " --> pdb=" O   GLU B 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 27
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE C  31 " --> pdb=" O   PRO C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 59
    Processing helix  chain 'C' and resid 84 through 93
    Processing helix  chain 'C' and resid 95 through 104
    Processing helix  chain 'C' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL C 120 " --> pdb=" O   LEU C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU C 124 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS C 125 " --> pdb=" O   ARG C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 173
    Processing helix  chain 'C' and resid 179 through 195
    Processing helix  chain 'C' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET C 249 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG C 268 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 290
    Processing helix  chain 'C' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU C 308 " --> pdb=" O   LEU C 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU C 310 " --> pdb=" O   ARG C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 317
    Processing helix  chain 'C' and resid 319 through 330
    Processing helix  chain 'C' and resid 380 through 386
    Processing helix  chain 'C' and resid 407 through 417
    Processing helix  chain 'C' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE C 424 " --> pdb=" O   PHE C 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER C 427 " --> pdb=" O   ALA C 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 429 " --> pdb=" O   GLU C 425 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 27
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 4.040A  pdb=" N   ILE D  31 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 59
    Processing helix  chain 'D' and resid 84 through 93
    Processing helix  chain 'D' and resid 95 through 104
    Processing helix  chain 'D' and resid 114 through 120
      removed outlier: 3.972A  pdb=" N   VAL D 120 " --> pdb=" O   LEU D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 127
      removed outlier: 4.416A  pdb=" N   LEU D 124 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LYS D 125 " --> pdb=" O   ARG D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 141
      removed outlier: 4.025A  pdb=" N   GLN D 134 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 173
    Processing helix  chain 'D' and resid 179 through 195
    Processing helix  chain 'D' and resid 206 through 260
      removed outlier: 4.881A  pdb=" N   LYS D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   MET D 249 " --> pdb=" O   GLN D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 262 through 280
      removed outlier: 4.172A  pdb=" N   ARG D 268 " --> pdb=" O   ASN D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 290
    Processing helix  chain 'D' and resid 293 through 310
      removed outlier: 3.699A  pdb=" N   LEU D 308 " --> pdb=" O   LEU D 304 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU D 310 " --> pdb=" O   ARG D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 317
    Processing helix  chain 'D' and resid 319 through 330
    Processing helix  chain 'D' and resid 380 through 386
    Processing helix  chain 'D' and resid 407 through 417
    Processing helix  chain 'D' and resid 417 through 429
      removed outlier: 3.883A  pdb=" N   ILE D 424 " --> pdb=" O   PHE D 420 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER D 427 " --> pdb=" O   ALA D 423 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA D 429 " --> pdb=" O   GLU D 425 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU A 401 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342
      removed outlier: 6.530A  pdb=" N   THR A 340 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA A 396 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU B 401 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR B 340 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA B 396 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU C 401 " --> pdb=" O   SER C 355 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR C 340 " --> pdb=" O   ALA C 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA C 396 " --> pdb=" O   THR C 340 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 335
      removed outlier: 6.544A  pdb=" N   GLU D 401 " --> pdb=" O   SER D 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 340 through 342
      removed outlier: 6.531A  pdb=" N   THR D 340 " --> pdb=" O   ALA D 396 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ALA D 396 " --> pdb=" O   THR D 340 " (cutoff:3.500A)

    893 hydrogen bonds defined for protein.
    2595 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.76

  Time building geometry restraints manager: 3.28 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4445
        2.86 -     3.37: 12000
        3.37 -     3.88: 17535
        3.88 -     4.39: 20739
        4.39 -     4.90: 30705
  Nonbonded interactions: 85424
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 101 "
            pdb=" OH  TYR A 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR D 101 "
            pdb=" OH  TYR D 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR C 101 "
            pdb=" OH  TYR C 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR B 101 "
            pdb=" OH  TYR B 115 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   ALA A 195 "
            pdb=" OG1 THR A 196 "
     model   vdw
     2.436 3.040
  ... (remaining 85419 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     24.650
  Find NCS groups from input model:        0.210
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.180
-------------------------------------------------------------------------------
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= 0.792
  Angle     :  1.557  32.963  15036  Z= 1.038
  Chirality :  0.138   1.499   1844
  Planarity :  0.011   0.129   1888
  Dihedral  :  8.803  66.342   3340
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.60 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  1.36 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.19), residues: 1516
  helix: -0.89 (0.13), residues: 1068
  sheet: -1.20 (0.47), residues: 68
  loop : -2.00 (0.31), residues: 380

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

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

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 403
  time to evaluate  : 1.442 
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: 0.2862
  time to fit residues: 151.0178
Evaluate side-chains
  189 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.183638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.154089 restraints weight = 20048.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.150250 restraints weight = 43840.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.150783 restraints weight = 39411.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10960  Z= 0.203
  Angle     :  0.544   7.205  15036  Z= 0.307
  Chirality :  0.039   0.128   1844
  Planarity :  0.006   0.065   1888
  Dihedral  :  4.270  18.580   1652
  Min Nonbonded Distance : 2.463

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.21), residues: 1516
  helix:  1.48 (0.15), residues: 1072
  sheet:  0.09 (0.65), residues: 52
  loop : -0.99 (0.30), residues: 392

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

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

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 1.171 
Fit side-chains
REVERT: A   28 PRO cc_start: 0.8974 (Cg_endo) cc_final: 0.8740 (Cg_exo)
REVERT: A  134 GLN cc_start: 0.7970 (tp40) cc_final: 0.7342 (tp-100)
REVERT: A  249 MET cc_start: 0.8826 (ttp) cc_final: 0.8378 (ttm)
REVERT: B  134 GLN cc_start: 0.7926 (tp40) cc_final: 0.7528 (tp40)
REVERT: B  249 MET cc_start: 0.8888 (ttp) cc_final: 0.8368 (ttm)
REVERT: C  162 TRP cc_start: 0.8562 (m-10) cc_final: 0.8036 (m100)
REVERT: C  249 MET cc_start: 0.8861 (ttp) cc_final: 0.8220 (ttm)
REVERT: D   28 PRO cc_start: 0.9011 (Cg_endo) cc_final: 0.8781 (Cg_exo)
REVERT: D  239 ASP cc_start: 0.8036 (t0) cc_final: 0.7826 (t0)
REVERT: D  249 MET cc_start: 0.8828 (ttp) cc_final: 0.8366 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.2439
  time to fit residues: 97.1906
Evaluate side-chains
  173 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 141 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 135 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 70 optimal weight:   30.0000
   chunk 111 optimal weight:   30.0000
   chunk 81 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0980
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4208 r_free = 0.4208 target = 0.179151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.153059 restraints weight = 21207.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.152450 restraints weight = 51154.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.150541 restraints weight = 36392.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10960  Z= 0.208
  Angle     :  0.490   6.701  15036  Z= 0.271
  Chirality :  0.038   0.124   1844
  Planarity :  0.004   0.051   1888
  Dihedral  :  3.809  15.594   1652
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.21), residues: 1516
  helix:  1.70 (0.15), residues: 1080
  sheet:  0.73 (0.79), residues: 48
  loop : -0.64 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  58 
 HIS   0.004   0.003   HIS C 161 
 PHE   0.022   0.002   PHE D 154 
 TYR   0.014   0.001   TYR D 188 
 ARG   0.004   0.001   ARG A 259 

*********************** 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
  237 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8819 (ttp) cc_final: 0.8243 (ttm)
REVERT: B  249 MET cc_start: 0.8857 (ttp) cc_final: 0.8231 (ttm)
REVERT: C  249 MET cc_start: 0.8903 (ttp) cc_final: 0.8344 (ttm)
REVERT: D  249 MET cc_start: 0.8800 (ttp) cc_final: 0.8151 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2146
  time to fit residues: 73.0840
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  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 113 optimal weight:    9.9990
   chunk 135 optimal weight:    5.9990
   chunk 144 optimal weight:   40.0000
   chunk 118 optimal weight:    8.9990
   chunk 94 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 106 optimal weight:   50.0000
   overall best weight:    1.0584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.180072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.151210 restraints weight = 20280.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.150551 restraints weight = 51849.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.151243 restraints weight = 43886.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10960  Z= 0.188
  Angle     :  0.483   6.601  15036  Z= 0.263
  Chirality :  0.038   0.121   1844
  Planarity :  0.003   0.041   1888
  Dihedral  :  3.677  14.795   1652
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.21), residues: 1516
  helix:  1.90 (0.15), residues: 1088
  sheet: -0.77 (0.54), residues: 88
  loop : -0.32 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  58 
 HIS   0.003   0.002   HIS B 161 
 PHE   0.016   0.002   PHE A  21 
 TYR   0.012   0.001   TYR C 188 
 ARG   0.002   0.000   ARG C 259 

*********************** 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
  219 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.7617 (tp40) cc_final: 0.7353 (tp40)
REVERT: B   54 LEU cc_start: 0.8910 (mt) cc_final: 0.8595 (tp)
REVERT: C   10 VAL cc_start: 0.8308 (t) cc_final: 0.8066 (t)
REVERT: C  134 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7079 (tp-100)
REVERT: C  249 MET cc_start: 0.8813 (ttp) cc_final: 0.8325 (ttm)
REVERT: D  249 MET cc_start: 0.8735 (ttp) cc_final: 0.8021 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2128
  time to fit residues: 66.6791
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  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 144 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 136 optimal weight:    0.8980
   chunk 123 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.180142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.151314 restraints weight = 20175.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.148566 restraints weight = 40653.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.149136 restraints weight = 34943.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.5622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10960  Z= 0.162
  Angle     :  0.454   6.665  15036  Z= 0.245
  Chirality :  0.037   0.121   1844
  Planarity :  0.003   0.037   1888
  Dihedral  :  3.465  14.083   1652
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.21), residues: 1516
  helix:  2.47 (0.14), residues: 1068
  sheet: -0.54 (0.55), residues: 88
  loop :  0.03 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  12 
 HIS   0.002   0.001   HIS C 161 
 PHE   0.025   0.002   PHE A 154 
 TYR   0.010   0.001   TYR C 188 
 ARG   0.004   0.000   ARG D 259 

*********************** 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
  210 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.7737 (tp40) cc_final: 0.7508 (tp-100)
REVERT: A  165 VAL cc_start: 0.9298 (t) cc_final: 0.9035 (p)
REVERT: B   10 VAL cc_start: 0.8478 (t) cc_final: 0.8256 (t)
REVERT: B  134 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7290 (tp40)
REVERT: B  165 VAL cc_start: 0.9313 (t) cc_final: 0.9058 (p)
REVERT: C   56 ILE cc_start: 0.8030 (mm) cc_final: 0.7830 (mm)
REVERT: C  138 LEU cc_start: 0.8343 (mt) cc_final: 0.8049 (pp)
REVERT: C  165 VAL cc_start: 0.9310 (t) cc_final: 0.9050 (p)
REVERT: C  249 MET cc_start: 0.8734 (ttp) cc_final: 0.8262 (ttm)
REVERT: D   56 ILE cc_start: 0.8077 (mm) cc_final: 0.7859 (mm)
REVERT: D   89 ASP cc_start: 0.7478 (m-30) cc_final: 0.7238 (t70)
REVERT: D  134 GLN cc_start: 0.7324 (tp-100) cc_final: 0.7047 (tp40)
REVERT: D  165 VAL cc_start: 0.9309 (t) cc_final: 0.9048 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2006
  time to fit residues: 61.5378
Evaluate side-chains
  164 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 102 optimal weight:   20.0000
   chunk 125 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 70 optimal weight:   50.0000
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.177886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.153127 restraints weight = 20238.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.151263 restraints weight = 31924.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.149020 restraints weight = 34402.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.5997

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= 0.248
  Angle     :  0.528   6.847  15036  Z= 0.280
  Chirality :  0.038   0.121   1844
  Planarity :  0.003   0.039   1888
  Dihedral  :  3.556  14.228   1652
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.21), residues: 1516
  helix:  2.47 (0.14), residues: 1060
  sheet: -0.55 (0.56), residues: 88
  loop : -0.43 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 155 
 HIS   0.005   0.003   HIS A 161 
 PHE   0.023   0.002   PHE B 154 
 TYR   0.016   0.002   TYR D 188 
 ARG   0.003   0.000   ARG B 259 

*********************** 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
  194 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.245 
Fit side-chains
REVERT: A  230 ASN cc_start: 0.9206 (t0) cc_final: 0.8927 (t0)
REVERT: B   56 ILE cc_start: 0.8064 (mm) cc_final: 0.7857 (mm)
REVERT: B  134 GLN cc_start: 0.7339 (tp-100) cc_final: 0.7070 (tp40)
REVERT: B  230 ASN cc_start: 0.9228 (t0) cc_final: 0.8926 (t0)
REVERT: C    7 ARG cc_start: 0.3898 (mtp180) cc_final: 0.3546 (ttm110)
REVERT: C  230 ASN cc_start: 0.9181 (t0) cc_final: 0.8923 (t0)
REVERT: D   56 ILE cc_start: 0.8081 (mm) cc_final: 0.7239 (mm)
REVERT: D  134 GLN cc_start: 0.7359 (tp-100) cc_final: 0.7063 (tp40)
REVERT: D  230 ASN cc_start: 0.9215 (t0) cc_final: 0.8939 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2133
  time to fit residues: 58.9933
Evaluate side-chains
  146 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   chunk 114 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 33 optimal weight:   50.0000
   chunk 94 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    2.7184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.173059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140953 restraints weight = 21127.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.138230 restraints weight = 30569.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.137379 restraints weight = 29260.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.6336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  10960  Z= 0.390
  Angle     :  0.668   7.417  15036  Z= 0.354
  Chirality :  0.041   0.133   1844
  Planarity :  0.004   0.039   1888
  Dihedral  :  3.968  16.103   1652
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.21), residues: 1516
  helix:  2.09 (0.15), residues: 1060
  sheet: -0.93 (0.56), residues: 88
  loop : -0.86 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 155 
 HIS   0.007   0.004   HIS D 161 
 PHE   0.028   0.003   PHE A  47 
 TYR   0.017   0.002   TYR D 188 
 ARG   0.003   0.001   ARG D 259 

*********************** 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
  179 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.249 
Fit side-chains
REVERT: A  134 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8082 (tp40)
REVERT: A  217 MET cc_start: 0.8867 (mtp) cc_final: 0.8660 (mtp)
REVERT: A  230 ASN cc_start: 0.9188 (t0) cc_final: 0.8923 (t0)
REVERT: B    7 ARG cc_start: 0.4227 (mtp180) cc_final: 0.3826 (ttm170)
REVERT: B   10 VAL cc_start: 0.8290 (t) cc_final: 0.8086 (t)
REVERT: B   97 GLU cc_start: 0.7384 (pm20) cc_final: 0.7180 (mm-30)
REVERT: B  134 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7373 (tp40)
REVERT: B  138 LEU cc_start: 0.9070 (pp) cc_final: 0.8836 (pp)
REVERT: B  217 MET cc_start: 0.8831 (mtp) cc_final: 0.8617 (mtp)
REVERT: B  230 ASN cc_start: 0.9173 (t0) cc_final: 0.8937 (t0)
REVERT: C  134 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7829 (tp40)
REVERT: C  217 MET cc_start: 0.8864 (mtp) cc_final: 0.8650 (mtp)
REVERT: C  230 ASN cc_start: 0.9167 (t0) cc_final: 0.8938 (t0)
REVERT: D  217 MET cc_start: 0.8870 (mtp) cc_final: 0.8662 (mtp)
REVERT: D  230 ASN cc_start: 0.9190 (t0) cc_final: 0.8909 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2309
  time to fit residues: 58.0998
Evaluate side-chains
  144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 96 optimal weight:    1.9990
   chunk 33 optimal weight:   50.0000
   chunk 60 optimal weight:    0.9980
   chunk 72 optimal weight:   40.0000
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 251 GLN
D 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.176771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144285 restraints weight = 21144.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141398 restraints weight = 31953.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.133387 restraints weight = 30840.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.6515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10960  Z= 0.198
  Angle     :  0.509   7.289  15036  Z= 0.267
  Chirality :  0.037   0.121   1844
  Planarity :  0.003   0.042   1888
  Dihedral  :  3.587  15.524   1652
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.21), residues: 1516
  helix:  2.41 (0.15), residues: 1068
  sheet: -0.71 (0.59), residues: 88
  loop : -0.64 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  85 
 HIS   0.002   0.001   HIS C 161 
 PHE   0.020   0.001   PHE B 154 
 TYR   0.009   0.001   TYR C 188 
 ARG   0.007   0.000   ARG B 270 

*********************** 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
  218 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ASP cc_start: 0.8168 (t70) cc_final: 0.7962 (m-30)
REVERT: A  134 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8071 (tp-100)
REVERT: A  165 VAL cc_start: 0.9361 (t) cc_final: 0.9137 (p)
REVERT: A  230 ASN cc_start: 0.9202 (t0) cc_final: 0.8932 (t0)
REVERT: B   89 ASP cc_start: 0.8020 (t70) cc_final: 0.7497 (m-30)
REVERT: B   97 GLU cc_start: 0.7606 (pm20) cc_final: 0.7127 (mm-30)
REVERT: B  134 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7300 (tp40)
REVERT: B  138 LEU cc_start: 0.9026 (pp) cc_final: 0.8424 (pp)
REVERT: B  162 TRP cc_start: 0.8306 (m-10) cc_final: 0.7965 (m100)
REVERT: B  165 VAL cc_start: 0.9334 (t) cc_final: 0.9037 (p)
REVERT: B  230 ASN cc_start: 0.9237 (t0) cc_final: 0.9025 (t0)
REVERT: B  274 MET cc_start: 0.8717 (mmm) cc_final: 0.8483 (mmm)
REVERT: C  134 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8059 (tp-100)
REVERT: C  165 VAL cc_start: 0.9366 (t) cc_final: 0.9149 (p)
REVERT: D   41 LEU cc_start: 0.8167 (mm) cc_final: 0.7707 (pt)
REVERT: D   97 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6910 (tp30)
REVERT: D  134 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7752 (tp40)
REVERT: D  165 VAL cc_start: 0.9369 (t) cc_final: 0.9136 (p)
REVERT: D  230 ASN cc_start: 0.9269 (t0) cc_final: 0.8999 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2474
  time to fit residues: 74.4078
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  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 103 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:   20.0000
   chunk 63 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 97 optimal weight:    0.2980
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.176691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.136084 restraints weight = 21577.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120309 restraints weight = 29702.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118704 restraints weight = 25999.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.6677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10960  Z= 0.191
  Angle     :  0.510   7.442  15036  Z= 0.265
  Chirality :  0.037   0.120   1844
  Planarity :  0.003   0.047   1888
  Dihedral  :  3.477  15.033   1652
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.21), residues: 1516
  helix:  2.49 (0.15), residues: 1072
  sheet: -0.79 (0.57), residues: 88
  loop : -0.47 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  12 
 HIS   0.002   0.002   HIS B 161 
 PHE   0.027   0.002   PHE B 154 
 TYR   0.010   0.001   TYR C 188 
 ARG   0.007   0.001   ARG B 270 

*********************** 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
  201 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7876 (tp-100)
REVERT: A  230 ASN cc_start: 0.9086 (t0) cc_final: 0.8810 (t0)
REVERT: A  248 LYS cc_start: 0.8851 (tppt) cc_final: 0.8381 (pptt)
REVERT: B   97 GLU cc_start: 0.7650 (pm20) cc_final: 0.7061 (mm-30)
REVERT: B  134 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8009 (tp40)
REVERT: B  138 LEU cc_start: 0.9046 (pp) cc_final: 0.8486 (pp)
REVERT: B  162 TRP cc_start: 0.8264 (m-10) cc_final: 0.7966 (m100)
REVERT: B  165 VAL cc_start: 0.9339 (t) cc_final: 0.9040 (p)
REVERT: C  134 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8417 (tp-100)
REVERT: C  165 VAL cc_start: 0.9385 (t) cc_final: 0.9185 (p)
REVERT: D    7 ARG cc_start: 0.3436 (mtp180) cc_final: 0.2957 (ttm110)
REVERT: D   41 LEU cc_start: 0.8046 (mm) cc_final: 0.7680 (pt)
REVERT: D  134 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8107 (tp40)
REVERT: D  230 ASN cc_start: 0.9105 (t0) cc_final: 0.8846 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2373
  time to fit residues: 66.9072
Evaluate side-chains
  156 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 130 optimal weight:    0.0770
   chunk 54 optimal weight:    0.6980
   chunk 117 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.178410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.135778 restraints weight = 21904.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.120814 restraints weight = 29401.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122320 restraints weight = 24215.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.6922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10960  Z= 0.158
  Angle     :  0.499   8.797  15036  Z= 0.253
  Chirality :  0.037   0.143   1844
  Planarity :  0.003   0.035   1888
  Dihedral  :  3.331  14.555   1652
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.22), residues: 1516
  helix:  2.69 (0.15), residues: 1068
  sheet: -0.69 (0.57), residues: 88
  loop : -0.45 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  22 
 HIS   0.002   0.001   HIS C 161 
 PHE   0.027   0.001   PHE B 154 
 TYR   0.009   0.001   TYR A 273 
 ARG   0.006   0.001   ARG B 270 

********************** 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
  219 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ASP cc_start: 0.8647 (t0) cc_final: 0.8122 (m-30)
REVERT: A  134 GLN cc_start: 0.8454 (tp-100) cc_final: 0.7817 (tp-100)
REVERT: A  138 LEU cc_start: 0.8727 (pp) cc_final: 0.8518 (pp)
REVERT: A  230 ASN cc_start: 0.9086 (t0) cc_final: 0.8838 (t0)
REVERT: A  248 LYS cc_start: 0.8783 (tppt) cc_final: 0.8213 (tmmt)
REVERT: B   89 ASP cc_start: 0.8525 (t70) cc_final: 0.8314 (m-30)
REVERT: B   97 GLU cc_start: 0.7572 (pm20) cc_final: 0.7013 (mm-30)
REVERT: B  134 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8225 (tp40)
REVERT: B  162 TRP cc_start: 0.8194 (m-10) cc_final: 0.7887 (m100)
REVERT: B  165 VAL cc_start: 0.9272 (t) cc_final: 0.9027 (p)
REVERT: C    7 ARG cc_start: 0.3731 (mtp180) cc_final: 0.3303 (ttm170)
REVERT: C   89 ASP cc_start: 0.8581 (t70) cc_final: 0.7860 (m-30)
REVERT: C  134 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8494 (tp40)
REVERT: D    7 ARG cc_start: 0.3856 (mtp180) cc_final: 0.3221 (ttm110)
REVERT: D   41 LEU cc_start: 0.7938 (mm) cc_final: 0.7289 (pt)
REVERT: D  134 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8071 (tp40)
REVERT: D  230 ASN cc_start: 0.9045 (t0) cc_final: 0.8794 (t0)
REVERT: D  253 ASP cc_start: 0.8660 (m-30) cc_final: 0.8347 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.2086
  time to fit residues: 65.8509
Evaluate side-chains
  170 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 146 optimal weight:   50.0000
   chunk 91 optimal weight:    0.6980
   chunk 111 optimal weight:   30.0000
   chunk 113 optimal weight:   30.0000
   chunk 22 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 137 optimal weight:    0.0050
   chunk 144 optimal weight:   40.0000
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.9398

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.174116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.133707 restraints weight = 21298.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117998 restraints weight = 30634.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117203 restraints weight = 26617.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.7006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  10960  Z= 0.300
  Angle     :  0.593   8.156  15036  Z= 0.309
  Chirality :  0.039   0.129   1844
  Planarity :  0.003   0.039   1888
  Dihedral  :  3.565  15.409   1652
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.21), residues: 1516
  helix:  2.35 (0.15), residues: 1068
  sheet: -0.96 (0.54), residues: 88
  loop : -0.56 (0.36), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  22 
 HIS   0.005   0.003   HIS A 161 
 PHE   0.024   0.002   PHE B 154 
 TYR   0.019   0.002   TYR D 273 
 ARG   0.007   0.001   ARG B 270 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2881.84 seconds
wall clock time: 52 minutes 31.35 seconds (3151.35 seconds total)