Starting phenix.real_space_refine
on Tue Mar  3 14:00:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cyv_27085/03_2026/8cyv_27085.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    3744      2.51       5
     N    1044      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5964
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, J, K, L, M, N
  Time building chain proxies: 0.65, per 1000 atoms: 0.11
  Number of scatterers: 5964
  At special positions: 0
  Unit cell: (81, 114.48, 48.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1176      8.00
     N    1044      7.00
     C    3744      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: 0.42
  Conformation dependent library (CDL) restraints added in 422.9 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 23
      removed outlier: 6.520A  pdb=" N   VAL C  16 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ALA B  19 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ALA C  18 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS B  21 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU C  20 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   LYS B  23 " --> pdb=" O   GLU C  20 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR C  22 " --> pdb=" O   LYS B  23 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL D  16 " --> pdb=" O   ALA C  17 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ALA C  19 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ALA D  18 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS C  21 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU D  20 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   LYS C  23 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR D  22 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL F  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ALA E  19 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ALA F  18 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   LYS E  21 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLU F  20 " --> pdb=" O   LYS E  21 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LYS E  23 " --> pdb=" O   GLU F  20 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   THR F  22 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42
      removed outlier: 6.475A  pdb=" N   LEU A  38 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   GLY B  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   VAL A  40 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU D  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   GLY E  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL D  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.266A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL D  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55
      removed outlier: 6.950A  pdb=" N   ALA C  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ALA D  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ALA F  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66
      removed outlier: 6.778A  pdb=" N   VAL C  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL B  66 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASN C  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL D  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL C  66 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASN D  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL F  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   VAL E  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ASN F  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71
      removed outlier: 6.521A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL D  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 79
      removed outlier: 6.393A  pdb=" N   ALA C  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ALA D  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ALA F  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 91
      removed outlier: 6.643A  pdb=" N   ALA C  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA D  90 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ALA F  90 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.609A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL D  95 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 17 through 23
      removed outlier: 6.795A  pdb=" N   ALA K  18 " --> pdb=" O   ALA J  19 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS J  21 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLU K  20 " --> pdb=" O   LYS J  21 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LYS J  23 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   THR K  22 " --> pdb=" O   LYS J  23 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ALA L  18 " --> pdb=" O   ALA K  19 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LYS K  21 " --> pdb=" O   ALA L  18 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLU L  20 " --> pdb=" O   LYS K  21 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   LYS K  23 " --> pdb=" O   GLU L  20 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR L  22 " --> pdb=" O   LYS K  23 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ALA N  18 " --> pdb=" O   ALA M  19 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   LYS M  21 " --> pdb=" O   ALA N  18 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLU N  20 " --> pdb=" O   LYS M  21 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LYS M  23 " --> pdb=" O   GLU N  20 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR N  22 " --> pdb=" O   LYS M  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 38 through 42
      removed outlier: 6.147A  pdb=" N   LEU I  38 " --> pdb=" O   TYR J  39 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   GLY J  41 " --> pdb=" O   LEU I  38 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL I  40 " --> pdb=" O   GLY J  41 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU L  38 " --> pdb=" O   TYR M  39 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   GLY M  41 " --> pdb=" O   LEU L  38 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL L  40 " --> pdb=" O   GLY M  41 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 48 through 49
      removed outlier: 6.453A  pdb=" N   VAL K  48 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL L  48 " --> pdb=" O   VAL K  49 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL N  48 " --> pdb=" O   VAL M  49 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 62 through 64
      removed outlier: 6.485A  pdb=" N   VAL K  63 " --> pdb=" O   THR J  64 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL L  63 " --> pdb=" O   THR K  64 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL N  63 " --> pdb=" O   THR M  64 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 70 through 71
      removed outlier: 6.107A  pdb=" N   VAL I  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   VAL L  70 " --> pdb=" O   VAL M  71 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 75 through 79
      removed outlier: 6.226A  pdb=" N   ALA K  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   GLN J  79 " --> pdb=" O   ALA K  76 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA K  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA L  76 " --> pdb=" O   VAL K  77 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   GLN K  79 " --> pdb=" O   ALA L  76 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ALA L  78 " --> pdb=" O   GLN K  79 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA N  76 " --> pdb=" O   VAL M  77 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   GLN M  79 " --> pdb=" O   ALA N  76 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA N  78 " --> pdb=" O   GLN M  79 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 86 through 91
      removed outlier: 6.365A  pdb=" N   SER I  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   ALA J  90 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA I  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   SER L  87 " --> pdb=" O   ILE M  88 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ALA M  90 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ALA L  89 " --> pdb=" O   ALA M  90 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 94 through 95
      removed outlier: 5.970A  pdb=" N   PHE K  94 " --> pdb=" O   VAL J  95 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   PHE L  94 " --> pdb=" O   VAL K  95 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   PHE N  94 " --> pdb=" O   VAL M  95 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    342 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: 0.77

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1032
        1.29 -     1.36: 924
        1.36 -     1.43: 204
        1.43 -     1.49: 1080
        1.49 -     1.56: 2736
  Bond restraints: 5976
  Sorted by residual:
  bond pdb=" N   LYS N  58 "
       pdb=" CA  LYS N  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.476 -0.014 1.52e-02 4.33e+03 8.97e-01
  bond pdb=" N   LYS J  58 "
       pdb=" CA  LYS J  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.82e-01
  bond pdb=" N   LYS I  58 "
       pdb=" CA  LYS I  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.40e-01
  bond pdb=" N   LYS L  58 "
       pdb=" CA  LYS L  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.475 -0.014 1.52e-02 4.33e+03 8.37e-01
  bond pdb=" C   GLU M  57 "
       pdb=" N   LYS M  58 "
    ideal  model  delta    sigma   weight residual
    1.332  1.345 -0.013 1.40e-02 5.10e+03 8.21e-01
  ... (remaining 5971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 7505
        1.03 -     2.06: 411
        2.06 -     3.09: 88
        3.09 -     4.12: 36
        4.12 -     5.15: 12
  Bond angle restraints: 8052
  Sorted by residual:
  angle pdb=" C   THR D  81 "
        pdb=" N   VAL D  82 "
        pdb=" CA  VAL D  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.12   -5.15 1.80e+00 3.09e-01 8.18e+00
  angle pdb=" C   THR E  81 "
        pdb=" N   VAL E  82 "
        pdb=" CA  VAL E  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.12   -5.15 1.80e+00 3.09e-01 8.18e+00
  angle pdb=" C   THR F  81 "
        pdb=" N   VAL F  82 "
        pdb=" CA  VAL F  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.16e+00
  angle pdb=" C   THR A  81 "
        pdb=" N   VAL A  82 "
        pdb=" CA  VAL A  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.16e+00
  angle pdb=" C   THR C  81 "
        pdb=" N   VAL C  82 "
        pdb=" CA  VAL C  82 "
      ideal   model   delta    sigma   weight residual
     121.97  127.11   -5.14 1.80e+00 3.09e-01 8.14e+00
  ... (remaining 8047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.63: 3184
       11.63 -    23.26: 271
       23.26 -    34.89: 49
       34.89 -    46.52: 12
       46.52 -    58.15: 12
  Dihedral angle restraints: 3528
    sinusoidal: 1188
      harmonic: 2340
  Sorted by residual:
  dihedral pdb=" CA  GLY M  73 "
           pdb=" C   GLY M  73 "
           pdb=" N   VAL M  74 "
           pdb=" CA  VAL M  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLY K  73 "
           pdb=" C   GLY K  73 "
           pdb=" N   VAL K  74 "
           pdb=" CA  VAL K  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLY I  73 "
           pdb=" C   GLY I  73 "
           pdb=" N   VAL I  74 "
           pdb=" CA  VAL I  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.06   17.94     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 3525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 449
       0.025 -    0.050: 309
       0.050 -    0.075: 103
       0.075 -    0.099: 84
       0.099 -    0.124: 123
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CA  ILE I  88 "
            pdb=" N   ILE I  88 "
            pdb=" C   ILE I  88 "
            pdb=" CB  ILE I  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE L  88 "
            pdb=" N   ILE L  88 "
            pdb=" C   ILE L  88 "
            pdb=" CB  ILE L  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  VAL K  40 "
            pdb=" N   VAL K  40 "
            pdb=" C   VAL K  40 "
            pdb=" CB  VAL K  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1065 not shown)

  Planarity restraints: 984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.08e+00
        pdb=" C   THR A  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR A  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A  82 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   THR D  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR D  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL D  82 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E  81 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   THR E  81 "    0.030 2.00e-02 2.50e+03
        pdb=" O   THR E  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL E  82 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 981 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 2394
        2.92 -     3.41: 4632
        3.41 -     3.91: 9727
        3.91 -     4.40: 9551
        4.40 -     4.90: 21742
  Nonbonded interactions: 48046
  Sorted by model distance:
  nonbonded pdb=" O   THR D  75 "
            pdb=" OG1 THR D  75 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" O   THR B  75 "
            pdb=" OG1 THR B  75 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" O   THR A  75 "
            pdb=" OG1 THR A  75 "
     model   vdw
     2.424 3.040
  nonbonded pdb=" O   THR E  75 "
            pdb=" OG1 THR E  75 "
     model   vdw
     2.424 3.040
  nonbonded pdb=" O   THR F  75 "
            pdb=" OG1 THR F  75 "
     model   vdw
     2.424 3.040
  ... (remaining 48041 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

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:             0.150
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.550
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
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      :  0.003   0.025   5976  Z= 0.160
  Angle     :  0.611   5.149   8052  Z= 0.358
  Chirality :  0.053   0.124   1068
  Planarity :  0.003   0.018    984
  Dihedral  : 10.014  58.153   2040
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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: -4.11 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR D  39 
 PHE   0.005   0.002   PHE M  94 
 HIS   0.001   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5976)
  covalent geometry    : angle       0.61068 ( 8052)
  hydrogen bonds       : bond        0.16075 (  114)
  hydrogen bonds       : angle       7.48079 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   79 GLN cc_start: 0.8325 (mt0) cc_final: 0.8090 (mt0)
REVERT: D   23 LYS cc_start: 0.8155 (tttt) cc_final: 0.7581 (tmtt)
REVERT: E   23 LYS cc_start: 0.8225 (tttt) cc_final: 0.7907 (tmtt)
REVERT: E   46 GLU cc_start: 0.8186 (tp30) cc_final: 0.7975 (tt0)
REVERT: L   43 LYS cc_start: 0.7951 (mttp) cc_final: 0.7616 (mmtp)
REVERT: L   46 GLU cc_start: 0.7504 (tt0) cc_final: 0.7278 (tm-30)
REVERT: M   43 LYS cc_start: 0.7818 (mttp) cc_final: 0.7587 (mttt)
REVERT: K   46 GLU cc_start: 0.7734 (tt0) cc_final: 0.7493 (tm-30)
REVERT: J   46 GLU cc_start: 0.7560 (tt0) cc_final: 0.7298 (tm-30)
REVERT: J   62 GLN cc_start: 0.7442 (tt0) cc_final: 0.7108 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0909
  time to fit residues: 16.7939
Evaluate side-chains
  117 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN
D  62 GLN
E  62 GLN
I  24 GLN
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  65 ASN
N  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  65 ASN
J  79 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.138564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.120149 restraints weight = 8726.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.123363 restraints weight = 4277.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.125501 restraints weight = 2616.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.126861 restraints weight = 1842.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.127814 restraints weight = 1457.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   5976  Z= 0.351
  Angle     :  0.731   5.751   8052  Z= 0.409
  Chirality :  0.051   0.139   1068
  Planarity :  0.004   0.017    984
  Dihedral  :  6.182  20.169    852
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 11.00 %
    Favored  : 85.83 %
  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: -4.23 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.032   0.005   TYR L  39 
 PHE   0.013   0.002   PHE C  94 
 HIS   0.006   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00745 ( 5976)
  covalent geometry    : angle       0.73113 ( 8052)
  hydrogen bonds       : bond        0.02380 (  114)
  hydrogen bonds       : angle       5.09970 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   97 LYS cc_start: 0.6885 (tttt) cc_final: 0.6368 (mttm)
REVERT: E   23 LYS cc_start: 0.8169 (tttt) cc_final: 0.7618 (tmtt)
REVERT: E   58 LYS cc_start: 0.7739 (tptm) cc_final: 0.6878 (mttp)
REVERT: C   45 LYS cc_start: 0.8394 (mttt) cc_final: 0.7896 (mtpt)
REVERT: I   72 THR cc_start: 0.8520 (p) cc_final: 0.8142 (p)
REVERT: L   46 GLU cc_start: 0.7283 (tt0) cc_final: 0.6944 (tm-30)
REVERT: M   43 LYS cc_start: 0.7819 (mttp) cc_final: 0.7284 (mtpt)
REVERT: M   46 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7191 (tm-30)
REVERT: K   46 GLU cc_start: 0.7310 (tt0) cc_final: 0.6910 (tm-30)
REVERT: J   45 LYS cc_start: 0.8170 (tttt) cc_final: 0.7105 (mttm)
REVERT: J   46 GLU cc_start: 0.7519 (tt0) cc_final: 0.7071 (tm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 153
  average time/residue: 0.1005
  time to fit residues: 19.0225
Evaluate side-chains
  151 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   22 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
E  62 GLN
E  79 GLN
C  62 GLN
C  79 GLN
I  65 ASN
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  79 GLN
N  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  79 GLN
K  65 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.139156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.121750 restraints weight = 8808.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.124782 restraints weight = 4378.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.126828 restraints weight = 2679.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.128133 restraints weight = 1893.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.129017 restraints weight = 1492.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5976  Z= 0.250
  Angle     :  0.608   8.151   8052  Z= 0.337
  Chirality :  0.051   0.160   1068
  Planarity :  0.003   0.029    984
  Dihedral  :  5.748  27.883    852
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.50 %
    Favored  : 80.83 %
  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: -4.35 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.003   TYR L  39 
 PHE   0.011   0.002   PHE D  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 5976)
  covalent geometry    : angle       0.60781 ( 8052)
  hydrogen bonds       : bond        0.02177 (  114)
  hydrogen bonds       : angle       4.88643 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.8803 (mttt) cc_final: 0.8267 (mttm)
REVERT: F   58 LYS cc_start: 0.7874 (tptm) cc_final: 0.7295 (mptt)
REVERT: F   97 LYS cc_start: 0.7045 (tttt) cc_final: 0.6603 (mttm)
REVERT: D   23 LYS cc_start: 0.7836 (tttt) cc_final: 0.7422 (tmtt)
REVERT: E   23 LYS cc_start: 0.8128 (tttt) cc_final: 0.7620 (tmtt)
REVERT: E   58 LYS cc_start: 0.7743 (tptm) cc_final: 0.6920 (mttp)
REVERT: C   45 LYS cc_start: 0.8386 (mttt) cc_final: 0.7862 (mtpt)
REVERT: L   43 LYS cc_start: 0.8247 (mptt) cc_final: 0.7799 (mmtp)
REVERT: L   46 GLU cc_start: 0.7319 (tt0) cc_final: 0.7060 (tm-30)
REVERT: L   58 LYS cc_start: 0.5846 (mtpp) cc_final: 0.5641 (mtmm)
REVERT: N   83 GLU cc_start: 0.7786 (tp30) cc_final: 0.7498 (tt0)
REVERT: M   43 LYS cc_start: 0.7789 (mttp) cc_final: 0.7308 (mtpt)
REVERT: M   46 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7248 (tm-30)
REVERT: K   46 GLU cc_start: 0.7188 (tt0) cc_final: 0.6911 (tm-30)
REVERT: K   65 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7858 (t0)
REVERT: J   45 LYS cc_start: 0.8221 (tttt) cc_final: 0.7230 (mttm)
REVERT: J   46 GLU cc_start: 0.7445 (tt0) cc_final: 0.7186 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1028
  time to fit residues: 19.9358
Evaluate side-chains
  161 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    0.2980
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    0.3980
   overall best weight:    4.5386

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 GLN
E  62 GLN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
N  65 ASN
N  79 GLN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  65 ASN
K  79 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.139912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.122610 restraints weight = 8781.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.125613 restraints weight = 4390.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.127593 restraints weight = 2689.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.128954 restraints weight = 1908.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.129846 restraints weight = 1498.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5976  Z= 0.218
  Angle     :  0.572   8.268   8052  Z= 0.319
  Chirality :  0.051   0.164   1068
  Planarity :  0.003   0.022    984
  Dihedral  :  5.574  24.021    852
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 17.33 %
    Favored  : 77.67 %
  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: -4.35 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.003   TYR K  39 
 PHE   0.011   0.002   PHE E  94 
 HIS   0.001   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5976)
  covalent geometry    : angle       0.57189 ( 8052)
  hydrogen bonds       : bond        0.01904 (  114)
  hydrogen bonds       : angle       4.80796 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: F   45 LYS cc_start: 0.8870 (mttt) cc_final: 0.8322 (mttm)
REVERT: F   58 LYS cc_start: 0.8056 (tptm) cc_final: 0.7449 (mptt)
REVERT: F   97 LYS cc_start: 0.7026 (tttt) cc_final: 0.6609 (mttm)
REVERT: D   23 LYS cc_start: 0.7602 (tttt) cc_final: 0.7313 (tmtt)
REVERT: E   23 LYS cc_start: 0.8103 (tttt) cc_final: 0.7599 (tmtt)
REVERT: E   58 LYS cc_start: 0.7768 (tptm) cc_final: 0.7012 (mttp)
REVERT: C   45 LYS cc_start: 0.8409 (mttt) cc_final: 0.7889 (mtpt)
REVERT: L   43 LYS cc_start: 0.8185 (mptt) cc_final: 0.7730 (mmtp)
REVERT: L   46 GLU cc_start: 0.7327 (tt0) cc_final: 0.7057 (tm-30)
REVERT: L   62 GLN cc_start: 0.7838 (mt0) cc_final: 0.7637 (tt0)
REVERT: N   83 GLU cc_start: 0.7874 (tp30) cc_final: 0.7611 (tt0)
REVERT: M   43 LYS cc_start: 0.7790 (mttp) cc_final: 0.7312 (mtpt)
REVERT: M   46 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: K   46 GLU cc_start: 0.7196 (tt0) cc_final: 0.6931 (tm-30)
REVERT: J   46 GLU cc_start: 0.7490 (tt0) cc_final: 0.7093 (tm-30)
  outliers start: 30
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0945
  time to fit residues: 18.4008
Evaluate side-chains
  166 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain M residue   45 LYS
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
N  65 ASN
** M  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.137429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.120173 restraints weight = 8910.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.123178 restraints weight = 4467.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.125207 restraints weight = 2744.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.126525 restraints weight = 1929.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.127437 restraints weight = 1515.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5976  Z= 0.263
  Angle     :  0.617   6.598   8052  Z= 0.344
  Chirality :  0.051   0.156   1068
  Planarity :  0.003   0.019    984
  Dihedral  :  5.792  24.205    852
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 17.33 %
    Favored  : 76.50 %
  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: -4.48 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.003   TYR K  39 
 PHE   0.013   0.002   PHE E  94 
 HIS   0.002   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 5976)
  covalent geometry    : angle       0.61729 ( 8052)
  hydrogen bonds       : bond        0.02133 (  114)
  hydrogen bonds       : angle       4.91295 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 0.200 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8953 (mttt) cc_final: 0.8541 (mttp)
REVERT: F   58 LYS cc_start: 0.8075 (tptm) cc_final: 0.7622 (mptt)
REVERT: F   97 LYS cc_start: 0.7043 (tttt) cc_final: 0.6591 (mttm)
REVERT: D   23 LYS cc_start: 0.7675 (tttt) cc_final: 0.7352 (tmtt)
REVERT: E   23 LYS cc_start: 0.8040 (tttt) cc_final: 0.7538 (tmtt)
REVERT: E   58 LYS cc_start: 0.7735 (tptm) cc_final: 0.7095 (mttp)
REVERT: C   45 LYS cc_start: 0.8423 (mttt) cc_final: 0.7940 (mtpt)
REVERT: L   46 GLU cc_start: 0.7266 (tt0) cc_final: 0.6982 (tm-30)
REVERT: N   83 GLU cc_start: 0.7840 (tp30) cc_final: 0.7614 (tt0)
REVERT: M   43 LYS cc_start: 0.7818 (mttp) cc_final: 0.7367 (mtpt)
REVERT: M   46 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: K   46 GLU cc_start: 0.7234 (tt0) cc_final: 0.6928 (tm-30)
REVERT: J   46 GLU cc_start: 0.7498 (tt0) cc_final: 0.7109 (tm-30)
REVERT: J   58 LYS cc_start: 0.5720 (tptp) cc_final: 0.5513 (mtmm)
  outliers start: 37
  outliers final: 29
  residues processed: 165
  average time/residue: 0.0869
  time to fit residues: 17.9917
Evaluate side-chains
  174 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain M residue   45 LYS
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    5.0166

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
C  62 GLN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.137797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.120525 restraints weight = 8864.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.123546 restraints weight = 4486.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.125493 restraints weight = 2748.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.126832 restraints weight = 1957.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.127762 restraints weight = 1537.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5976  Z= 0.232
  Angle     :  0.586   6.825   8052  Z= 0.326
  Chirality :  0.051   0.161   1068
  Planarity :  0.002   0.018    984
  Dihedral  :  5.672  23.775    852
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 17.33 %
    Favored  : 76.00 %
  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: -4.41 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.017   0.003   TYR K  39 
 PHE   0.013   0.002   PHE E  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 5976)
  covalent geometry    : angle       0.58620 ( 8052)
  hydrogen bonds       : bond        0.01997 (  114)
  hydrogen bonds       : angle       4.84278 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.221 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8868 (mttt) cc_final: 0.8567 (mttp)
REVERT: F   58 LYS cc_start: 0.7994 (tptm) cc_final: 0.7680 (mptt)
REVERT: F   97 LYS cc_start: 0.7122 (tttt) cc_final: 0.6556 (mttm)
REVERT: D   23 LYS cc_start: 0.7687 (tttt) cc_final: 0.7267 (tmtt)
REVERT: E   23 LYS cc_start: 0.8110 (tttt) cc_final: 0.7561 (tmtt)
REVERT: C   45 LYS cc_start: 0.8419 (mttt) cc_final: 0.7907 (mtpt)
REVERT: L   46 GLU cc_start: 0.7264 (tt0) cc_final: 0.6934 (tm-30)
REVERT: M   43 LYS cc_start: 0.7818 (mttp) cc_final: 0.7351 (mtpt)
REVERT: M   46 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7318 (tm-30)
REVERT: M   65 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7721 (t0)
REVERT: K   46 GLU cc_start: 0.7228 (tt0) cc_final: 0.6863 (tm-30)
REVERT: J   46 GLU cc_start: 0.7479 (tt0) cc_final: 0.7059 (tm-30)
  outliers start: 40
  outliers final: 31
  residues processed: 170
  average time/residue: 0.0880
  time to fit residues: 18.6740
Evaluate side-chains
  182 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain M residue   65 ASN
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   58 LYS
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0040
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    3.8000

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.139815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.122375 restraints weight = 8725.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.125466 restraints weight = 4390.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.127428 restraints weight = 2694.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.128759 restraints weight = 1920.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.129671 restraints weight = 1514.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5976  Z= 0.186
  Angle     :  0.547   6.207   8052  Z= 0.305
  Chirality :  0.051   0.165   1068
  Planarity :  0.002   0.018    984
  Dihedral  :  5.402  20.898    852
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 17.50 %
    Favored  : 75.50 %
  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: -4.28 (0.21), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR M  39 
 PHE   0.011   0.002   PHE E  94 
 HIS   0.002   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5976)
  covalent geometry    : angle       0.54679 ( 8052)
  hydrogen bonds       : bond        0.01747 (  114)
  hydrogen bonds       : angle       4.70644 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 149
  time to evaluate  : 0.156 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8877 (mttt) cc_final: 0.8581 (mttp)
REVERT: F   58 LYS cc_start: 0.8095 (tptm) cc_final: 0.7645 (mptt)
REVERT: F   97 LYS cc_start: 0.7072 (tttt) cc_final: 0.6560 (mttm)
REVERT: D   23 LYS cc_start: 0.7600 (tttt) cc_final: 0.7196 (tmtt)
REVERT: E   23 LYS cc_start: 0.8024 (tttt) cc_final: 0.7452 (tmtt)
REVERT: C   38 LEU cc_start: 0.8679 (mp) cc_final: 0.8464 (mt)
REVERT: C   45 LYS cc_start: 0.8402 (mttt) cc_final: 0.7889 (mtpt)
REVERT: I   62 GLN cc_start: 0.7835 (mt0) cc_final: 0.7618 (mt0)
REVERT: L   46 GLU cc_start: 0.7181 (tt0) cc_final: 0.6928 (tm-30)
REVERT: M   43 LYS cc_start: 0.7823 (mttp) cc_final: 0.7356 (mtpt)
REVERT: M   46 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: K   46 GLU cc_start: 0.7253 (tt0) cc_final: 0.6852 (tm-30)
REVERT: J   46 GLU cc_start: 0.7450 (tt0) cc_final: 0.7063 (tm-30)
  outliers start: 42
  outliers final: 32
  residues processed: 169
  average time/residue: 0.0851
  time to fit residues: 18.0566
Evaluate side-chains
  180 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain N residue   65 ASN
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 GLN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
M  65 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.141013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.123432 restraints weight = 8669.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.126534 restraints weight = 4334.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.128509 restraints weight = 2655.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.129849 restraints weight = 1890.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.130685 restraints weight = 1489.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5976  Z= 0.153
  Angle     :  0.521   7.307   8052  Z= 0.287
  Chirality :  0.051   0.180   1068
  Planarity :  0.002   0.018    984
  Dihedral  :  5.131  20.490    852
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 18.50 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.15 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.002   TYR M  39 
 PHE   0.011   0.002   PHE E  94 
 HIS   0.001   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5976)
  covalent geometry    : angle       0.52101 ( 8052)
  hydrogen bonds       : bond        0.01496 (  114)
  hydrogen bonds       : angle       4.51460 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.208 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8865 (mttt) cc_final: 0.8572 (mttp)
REVERT: F   58 LYS cc_start: 0.8071 (tptm) cc_final: 0.7673 (mptt)
REVERT: F   97 LYS cc_start: 0.7077 (tttt) cc_final: 0.6569 (mttm)
REVERT: D   23 LYS cc_start: 0.7447 (tttt) cc_final: 0.7109 (tmtt)
REVERT: E   23 LYS cc_start: 0.7923 (tttt) cc_final: 0.7354 (tmtt)
REVERT: C   45 LYS cc_start: 0.8416 (mttt) cc_final: 0.7964 (mtpt)
REVERT: I   62 GLN cc_start: 0.7794 (mt0) cc_final: 0.7590 (mt0)
REVERT: M   43 LYS cc_start: 0.7811 (mttp) cc_final: 0.7362 (mtpt)
REVERT: M   46 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7378 (tm-30)
REVERT: K   46 GLU cc_start: 0.7229 (tt0) cc_final: 0.6929 (tm-30)
REVERT: J   46 GLU cc_start: 0.7409 (tt0) cc_final: 0.7147 (tm-30)
  outliers start: 38
  outliers final: 25
  residues processed: 165
  average time/residue: 0.0860
  time to fit residues: 17.7965
Evaluate side-chains
  173 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain K residue   58 LYS
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 56 optimal weight:   30.0000
   chunk 19 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  65 ASN
N  65 ASN
M  65 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.137461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 19)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.119912 restraints weight = 8842.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.122923 restraints weight = 4446.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.124910 restraints weight = 2741.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.126164 restraints weight = 1955.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.127093 restraints weight = 1558.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5976  Z= 0.246
  Angle     :  0.624   7.280   8052  Z= 0.346
  Chirality :  0.051   0.178   1068
  Planarity :  0.003   0.017    984
  Dihedral  :  5.646  22.066    852
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.19 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 19.00 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.22 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.003   TYR N  39 
 PHE   0.014   0.002   PHE E  94 
 HIS   0.002   0.001   HIS M  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 5976)
  covalent geometry    : angle       0.62393 ( 8052)
  hydrogen bonds       : bond        0.01977 (  114)
  hydrogen bonds       : angle       4.83507 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 0.204 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8861 (mttt) cc_final: 0.8555 (mttp)
REVERT: F   97 LYS cc_start: 0.7086 (tttt) cc_final: 0.6555 (mttm)
REVERT: D   23 LYS cc_start: 0.7511 (tttt) cc_final: 0.7142 (tmtt)
REVERT: E   23 LYS cc_start: 0.7911 (tttt) cc_final: 0.7379 (tmtt)
REVERT: C   45 LYS cc_start: 0.8468 (mttt) cc_final: 0.7954 (mtpt)
REVERT: I   62 GLN cc_start: 0.7954 (mt0) cc_final: 0.7742 (mt0)
REVERT: M   43 LYS cc_start: 0.7836 (mttp) cc_final: 0.7374 (mtpt)
REVERT: M   46 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7438 (tm-30)
REVERT: K   46 GLU cc_start: 0.7225 (tt0) cc_final: 0.6963 (tm-30)
REVERT: J   46 GLU cc_start: 0.7386 (tt0) cc_final: 0.7055 (tm-30)
  outliers start: 35
  outliers final: 29
  residues processed: 170
  average time/residue: 0.0883
  time to fit residues: 18.9107
Evaluate side-chains
  179 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain D residue   24 GLN
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   62 GLN
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain K residue   22 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 54 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0570
   chunk 9 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    1.3502

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  65 ASN
L  65 ASN
N  65 ASN
M  65 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.144753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.125726 restraints weight = 8277.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.129010 restraints weight = 4170.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.131184 restraints weight = 2564.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.132592 restraints weight = 1820.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.133499 restraints weight = 1442.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.5065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5976  Z= 0.105
  Angle     :  0.514   8.650   8052  Z= 0.281
  Chirality :  0.052   0.205   1068
  Planarity :  0.002   0.020    984
  Dihedral  :  4.778  16.738    852
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.13 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.00 %
    Favored  : 73.83 %
  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: -3.96 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.001   TYR M  39 
 PHE   0.010   0.002   PHE E  94 
 HIS   0.002   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 5976)
  covalent geometry    : angle       0.51419 ( 8052)
  hydrogen bonds       : bond        0.01206 (  114)
  hydrogen bonds       : angle       4.36368 (  342)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.4751 (OUTLIER) cc_final: 0.4472 (pttm)
REVERT: F   45 LYS cc_start: 0.8884 (mttt) cc_final: 0.8493 (mttp)
REVERT: F   97 LYS cc_start: 0.7064 (tttt) cc_final: 0.6540 (mttm)
REVERT: D   23 LYS cc_start: 0.7361 (tttt) cc_final: 0.6981 (tmtt)
REVERT: E   23 LYS cc_start: 0.7908 (tttt) cc_final: 0.7331 (tmtt)
REVERT: C   45 LYS cc_start: 0.8351 (mttt) cc_final: 0.7836 (mtpt)
REVERT: I   62 GLN cc_start: 0.7821 (mt0) cc_final: 0.7599 (mt0)
REVERT: M   43 LYS cc_start: 0.7822 (mttp) cc_final: 0.7363 (mtpt)
REVERT: M   46 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7435 (tm-30)
REVERT: J   46 GLU cc_start: 0.7413 (tt0) cc_final: 0.7113 (tm-30)
  outliers start: 25
  outliers final: 14
  residues processed: 167
  average time/residue: 0.0864
  time to fit residues: 18.1018
Evaluate side-chains
  166 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain L residue   44 THR
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   55 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 49 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 56 optimal weight:   30.0000
   chunk 80 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   chunk 20 optimal weight:   30.0000
   overall best weight:   12.9994

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

Flipped N/Q/H residues before XYZ refinement:
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
C  65 ASN
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  79 GLN
L  65 ASN
N  65 ASN
M  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.131458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.114172 restraints weight = 9256.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.117059 restraints weight = 4790.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.118935 restraints weight = 3001.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.120172 restraints weight = 2159.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.121014 restraints weight = 1720.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.080   5976  Z= 0.542
  Angle     :  0.966   7.893   8052  Z= 0.538
  Chirality :  0.059   0.189   1068
  Planarity :  0.005   0.019    984
  Dihedral  :  7.018  28.532    852
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  : 13.36 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 20.33 %
    Favored  : 74.67 %
  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: -4.57 (0.20), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.16), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.032   0.005   TYR K  39 
 PHE   0.019   0.003   PHE E  94 
 HIS   0.006   0.002   HIS K  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01155 ( 5976)
  covalent geometry    : angle       0.96620 ( 8052)
  hydrogen bonds       : bond        0.03629 (  114)
  hydrogen bonds       : angle       5.67912 (  342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 947.19 seconds
wall clock time: 17 minutes 13.16 seconds (1033.16 seconds total)