Starting phenix.real_space_refine
on Tue Mar  3 13:12:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xyp_10651/03_2026/6xyp_10651.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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    3085      2.51       5
     N     865      2.21       5
     O    1005      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 4955
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 549
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
    Chain: "B"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 442
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Restraints were copied for chains:
    C, E, G, I, D, F, H, J
  Time building chain proxies: 0.65, per 1000 atoms: 0.13
  Number of scatterers: 4955
  At special positions: 0
  Unit cell: (105.8, 80.5, 41.4, 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    1005      8.00
     N     865      7.00
     C    3085      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: 0.40
  Conformation dependent library (CDL) restraints added in 309.3 milliseconds
  

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18
      removed outlier: 6.542A  pdb=" N   VAL A  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL G  16 " --> pdb=" O   ALA I  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 30
      removed outlier: 6.717A  pdb=" N   GLY C  25 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   GLU E  28 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA C  27 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   ALA E  30 " --> pdb=" O   ALA C  27 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA C  29 " --> pdb=" O   ALA E  30 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLY A  25 " --> pdb=" O   VAL I  26 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   GLU I  28 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ALA A  27 " --> pdb=" O   GLU I  28 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA I  30 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ALA A  29 " --> pdb=" O   ALA I  30 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 40
      removed outlier: 6.254A  pdb=" N   LEU A  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LEU G  38 " --> pdb=" O   TYR I  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 52
      removed outlier: 9.001A  pdb=" N   LYS C  45 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   VAL E  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   GLY C  47 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   HIS E  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   VAL C  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL E  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLY C  51 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLU A  46 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLY E  47 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL A  52 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 8.965A  pdb=" N   LYS A  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   VAL I  48 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   HIS I  50 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL A  49 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL I  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   GLY A  51 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   GLU G  46 " --> pdb=" O   LYS I  45 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLY I  47 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL G  52 " --> pdb=" O   GLY I  51 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.475A  pdb=" N   THR C  59 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLN E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLU C  61 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   THR A  59 " --> pdb=" O   LYS I  60 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLN I  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLU A  61 " --> pdb=" O   GLN I  62 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LYS G  58 " --> pdb=" O   THR I  59 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   GLU I  61 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LYS G  60 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL I  63 " --> pdb=" O   LYS G  60 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN G  62 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71
      removed outlier: 6.365A  pdb=" N   ALA A  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ALA G  69 " --> pdb=" O   VAL I  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81
      removed outlier: 6.332A  pdb=" N   ALA C  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   GLN E  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   THR E  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LYS C  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ALA A  76 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   GLN I  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ALA A  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   THR I  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LYS A  80 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 91
      removed outlier: 6.258A  pdb=" N   ALA C  90 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ALA A  90 " --> pdb=" O   ALA I  91 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40
      removed outlier: 6.496A  pdb=" N   TYR D  39 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   TYR B  39 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 52
      removed outlier: 6.880A  pdb=" N   VAL D  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL F  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   HIS D  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLY F  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   LYS B  45 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   VAL F  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   GLY B  47 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 10.011A  pdb=" N   HIS F  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 9.110A  pdb=" N   VAL B  49 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   VAL F  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   GLY B  51 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL B  48 " --> pdb=" O   GLY J  47 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL J  49 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   HIS B  50 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   GLY J  51 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LYS H  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   VAL J  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY H  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
      removed outlier: 9.649A  pdb=" N   HIS J  50 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 8.742A  pdb=" N   VAL H  49 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 8.830A  pdb=" N   VAL J  52 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   GLY H  51 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 55 through 57
      removed outlier: 6.386A  pdb=" N   ALA D  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ALA B  56 " --> pdb=" O   GLU J  57 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 66
      removed outlier: 6.284A  pdb=" N   GLN B  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   ASN F  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   THR B  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   GLN H  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.627A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL B  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77
      removed outlier: 6.539A  pdb=" N   ALA D  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ALA B  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.787A  pdb=" N   LYS D  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LYS B  80 " --> pdb=" O   THR J  81 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 96
      removed outlier: 6.278A  pdb=" N   VAL B  95 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL H  95 " --> pdb=" O   LYS J  96 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 33 through 34
      removed outlier: 6.655A  pdb=" N   THR G  33 " --> pdb=" O   LYS I  34 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    79 hydrogen bonds defined for protein.
    237 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: 0.79

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 885
        1.28 -     1.35: 775
        1.35 -     1.41: 170
        1.41 -     1.48: 830
        1.48 -     1.54: 2315
  Bond restraints: 4975
  Sorted by residual:
  bond pdb=" CB  VAL J  37 "
       pdb=" CG2 VAL J  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.03e+00
  bond pdb=" CB  VAL F  37 "
       pdb=" CG2 VAL F  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.01e+00
  bond pdb=" CB  VAL H  37 "
       pdb=" CG2 VAL H  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 1.99e+00
  bond pdb=" CB  VAL B  37 "
       pdb=" CG2 VAL B  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 1.99e+00
  bond pdb=" CB  VAL D  37 "
       pdb=" CG2 VAL D  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.89e+00
  ... (remaining 4970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 5807
        0.86 -     1.71: 755
        1.71 -     2.57: 118
        2.57 -     3.43: 35
        3.43 -     4.28: 5
  Bond angle restraints: 6720
  Sorted by residual:
  angle pdb=" N   LYS E  23 "
        pdb=" CA  LYS E  23 "
        pdb=" C   LYS E  23 "
      ideal   model   delta    sigma   weight residual
     113.88  110.65    3.23 1.23e+00 6.61e-01 6.89e+00
  angle pdb=" N   LYS G  23 "
        pdb=" CA  LYS G  23 "
        pdb=" C   LYS G  23 "
      ideal   model   delta    sigma   weight residual
     113.88  110.66    3.22 1.23e+00 6.61e-01 6.84e+00
  angle pdb=" N   LYS I  23 "
        pdb=" CA  LYS I  23 "
        pdb=" C   LYS I  23 "
      ideal   model   delta    sigma   weight residual
     113.88  110.67    3.21 1.23e+00 6.61e-01 6.79e+00
  angle pdb=" N   LYS A  23 "
        pdb=" CA  LYS A  23 "
        pdb=" C   LYS A  23 "
      ideal   model   delta    sigma   weight residual
     113.88  110.69    3.19 1.23e+00 6.61e-01 6.75e+00
  angle pdb=" N   LYS C  23 "
        pdb=" CA  LYS C  23 "
        pdb=" C   LYS C  23 "
      ideal   model   delta    sigma   weight residual
     113.88  110.71    3.17 1.23e+00 6.61e-01 6.65e+00
  ... (remaining 6715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.88: 2545
       13.88 -    27.76: 275
       27.76 -    41.63: 50
       41.63 -    55.51: 28
       55.51 -    69.39: 12
  Dihedral angle restraints: 2910
    sinusoidal: 965
      harmonic: 1945
  Sorted by residual:
  dihedral pdb=" CA  ALA I  78 "
           pdb=" C   ALA I  78 "
           pdb=" N   GLN I  79 "
           pdb=" CA  GLN I  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.79  -16.21     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  ALA A  78 "
           pdb=" C   ALA A  78 "
           pdb=" N   GLN A  79 "
           pdb=" CA  GLN A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.79  -16.21     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  ALA E  78 "
           pdb=" C   ALA E  78 "
           pdb=" N   GLN E  79 "
           pdb=" CA  GLN E  79 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.80  -16.20     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 2907 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 580
       0.047 -    0.094: 216
       0.094 -    0.142: 69
       0.142 -    0.189: 0
       0.189 -    0.236: 5
  Chirality restraints: 870
  Sorted by residual:
  chirality pdb=" CB  VAL H  37 "
            pdb=" CA  VAL H  37 "
            pdb=" CG1 VAL H  37 "
            pdb=" CG2 VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  VAL J  37 "
            pdb=" CA  VAL J  37 "
            pdb=" CG1 VAL J  37 "
            pdb=" CG2 VAL J  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  VAL F  37 "
            pdb=" CA  VAL F  37 "
            pdb=" CG1 VAL F  37 "
            pdb=" CG2 VAL F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 867 not shown)

  Planarity restraints: 845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  94 "    0.009 2.00e-02 2.50e+03   6.85e-03 8.21e-01
        pdb=" CG  PHE F  94 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  94 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  94 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  94 "    0.009 2.00e-02 2.50e+03   6.77e-03 8.03e-01
        pdb=" CG  PHE D  94 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  94 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  94 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "    0.009 2.00e-02 2.50e+03   6.72e-03 7.91e-01
        pdb=" CG  PHE B  94 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "    0.001 2.00e-02 2.50e+03
  ... (remaining 842 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 213
        2.70 -     3.25: 4728
        3.25 -     3.80: 7594
        3.80 -     4.35: 9574
        4.35 -     4.90: 18788
  Nonbonded interactions: 40897
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  28 "
            pdb=" NZ  LYS F  60 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" OE2 GLU A  28 "
            pdb=" NZ  LYS H  60 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OE1 GLU A  28 "
            pdb=" NZ  LYS J  60 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE1 GLU E  28 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" NZ  LYS H  60 "
            pdb=" OE1 GLU I  28 "
     model   vdw
     2.337 3.120
  ... (remaining 40892 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
}

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 individual isotropic
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:             0.820
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.930
  Find NCS groups from input model:        0.050
  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:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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      :  0.008   0.047   4975  Z= 0.388
  Angle     :  0.643   4.284   6720  Z= 0.388
  Chirality :  0.055   0.236    870
  Planarity :  0.002   0.007    845
  Dihedral  : 13.985  69.389   1690
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.04 (0.22), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.16), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR G  39 
 PHE   0.015   0.003   PHE F  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00836 ( 4975)
  covalent geometry    : angle       0.64323 ( 6720)
  hydrogen bonds       : bond        0.17122 (   79)
  hydrogen bonds       : angle       7.70385 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8604 (ttmm)
REVERT: B   58 LYS cc_start: 0.8494 (mttt) cc_final: 0.8054 (mttt)
REVERT: E   32 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8469 (ttmm)
REVERT: F   58 LYS cc_start: 0.8481 (mttt) cc_final: 0.8129 (mttt)
REVERT: G   20 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7430 (mp0)
REVERT: G   43 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7197 (mttt)
REVERT: H   60 LYS cc_start: 0.8161 (mppt) cc_final: 0.7388 (mptt)
REVERT: I   28 GLU cc_start: 0.7471 (tt0) cc_final: 0.7178 (mt-10)
REVERT: I   35 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8158 (mm-30)
REVERT: I   46 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: J   60 LYS cc_start: 0.8933 (mppt) cc_final: 0.8419 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1052
  time to fit residues: 9.0905
Evaluate side-chains
  62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
D  62 GLN
H  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.123801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.093537 restraints weight = 5531.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.93
r_work: 0.3175 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4975  Z= 0.139
  Angle     :  0.449   5.021   6720  Z= 0.252
  Chirality :  0.051   0.122    870
  Planarity :  0.002   0.008    845
  Dihedral  :  4.961  16.171    725
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.02 %
    Favored  : 88.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.24), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.18), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR E  39 
 PHE   0.012   0.001   PHE F  94 
 HIS   0.007   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4975)
  covalent geometry    : angle       0.44903 ( 6720)
  hydrogen bonds       : bond        0.01714 (   79)
  hydrogen bonds       : angle       4.73177 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.162 
Fit side-chains
REVERT: C   35 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7110 (pt0)
REVERT: E   32 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8356 (ttmm)
REVERT: E   35 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: G   43 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7115 (mttt)
REVERT: H   60 LYS cc_start: 0.9101 (mppt) cc_final: 0.8734 (mptt)
REVERT: H   97 LYS cc_start: 0.8465 (mttt) cc_final: 0.8212 (mttt)
REVERT: J   60 LYS cc_start: 0.8982 (mppt) cc_final: 0.8433 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1069
  time to fit residues: 7.7597
Evaluate side-chains
  58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
C  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.119788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.089933 restraints weight = 5576.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.79
r_work: 0.3160 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   4975  Z= 0.339
  Angle     :  0.566   7.148   6720  Z= 0.313
  Chirality :  0.053   0.125    870
  Planarity :  0.002   0.008    845
  Dihedral  :  5.301  15.855    725
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.65 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.20 (0.24), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.18), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR A  39 
 PHE   0.017   0.003   PHE F  94 
 HIS   0.008   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 ( 4975)
  covalent geometry    : angle       0.56572 ( 6720)
  hydrogen bonds       : bond        0.01969 (   79)
  hydrogen bonds       : angle       4.65537 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.188 
Fit side-chains
REVERT: C   35 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8401 (mm-30)
REVERT: E   28 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7512 (mt-10)
REVERT: E   32 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8397 (ttmm)
REVERT: E   35 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8279 (mm-30)
REVERT: G   43 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7213 (mttt)
REVERT: H   60 LYS cc_start: 0.9129 (mppt) cc_final: 0.8665 (mptt)
REVERT: I   28 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7491 (mt-10)
REVERT: J   60 LYS cc_start: 0.9135 (mppt) cc_final: 0.8490 (mptt)
  outliers start: 12
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0973
  time to fit residues: 7.8799
Evaluate side-chains
  72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   28 GLU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 28 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
G  50 HIS
J  50 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.124852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095530 restraints weight = 5427.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.72
r_work: 0.3276 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4975  Z= 0.115
  Angle     :  0.426   5.606   6720  Z= 0.237
  Chirality :  0.050   0.123    870
  Planarity :  0.001   0.005    845
  Dihedral  :  4.752  15.566    725
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 15.71 %
    Favored  : 83.67 %
  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: -3.76 (0.25), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.19), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR E  39 
 PHE   0.009   0.001   PHE F  94 
 HIS   0.004   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4975)
  covalent geometry    : angle       0.42613 ( 6720)
  hydrogen bonds       : bond        0.01297 (   79)
  hydrogen bonds       : angle       4.13032 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.133 
Fit side-chains
REVERT: B   97 LYS cc_start: 0.8507 (mttt) cc_final: 0.8214 (mttt)
REVERT: C   35 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7074 (pt0)
REVERT: G   35 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8473 (mm-30)
REVERT: G   43 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7204 (mttt)
REVERT: H   60 LYS cc_start: 0.9083 (mppt) cc_final: 0.8816 (mptt)
REVERT: J   60 LYS cc_start: 0.8959 (mppt) cc_final: 0.8681 (mptt)
  outliers start: 3
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0985
  time to fit residues: 7.2216
Evaluate side-chains
  60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 49 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
E  79 GLN
F  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.118461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.088483 restraints weight = 5722.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.81
r_work: 0.3148 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042   4975  Z= 0.399
  Angle     :  0.596   7.489   6720  Z= 0.333
  Chirality :  0.053   0.120    870
  Planarity :  0.002   0.008    845
  Dihedral  :  5.357  15.759    725
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.12 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.25), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.19), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR A  39 
 PHE   0.017   0.003   PHE F  94 
 HIS   0.009   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00878 ( 4975)
  covalent geometry    : angle       0.59581 ( 6720)
  hydrogen bonds       : bond        0.01868 (   79)
  hydrogen bonds       : angle       4.53253 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: B   60 LYS cc_start: 0.8798 (mptt) cc_final: 0.8053 (mptt)
REVERT: C   28 GLU cc_start: 0.8100 (tt0) cc_final: 0.7759 (mt-10)
REVERT: C   35 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8389 (mm-30)
REVERT: E   28 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7251 (mt-10)
REVERT: E   32 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8348 (ttmm)
REVERT: G   43 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7203 (mttt)
REVERT: J   60 LYS cc_start: 0.9157 (mppt) cc_final: 0.8467 (mptt)
  outliers start: 18
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0987
  time to fit residues: 8.7563
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   28 GLU
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0050
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.2002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.123971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.093888 restraints weight = 5612.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.87
r_work: 0.3265 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4975  Z= 0.132
  Angle     :  0.440   5.987   6720  Z= 0.242
  Chirality :  0.050   0.125    870
  Planarity :  0.001   0.005    845
  Dihedral  :  4.843  15.628    725
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 18.37 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.57 (0.26), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR A  39 
 PHE   0.010   0.001   PHE F  94 
 HIS   0.004   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4975)
  covalent geometry    : angle       0.43999 ( 6720)
  hydrogen bonds       : bond        0.01290 (   79)
  hydrogen bonds       : angle       4.07517 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B   97 LYS cc_start: 0.8558 (mttt) cc_final: 0.8261 (mttt)
REVERT: C   35 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: E   32 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8194 (ttmm)
REVERT: G   43 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7209 (mttt)
REVERT: H   97 LYS cc_start: 0.8557 (mttt) cc_final: 0.7327 (mmmt)
REVERT: I   28 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7776 (mt-10)
REVERT: J   60 LYS cc_start: 0.8988 (mppt) cc_final: 0.8726 (mptt)
  outliers start: 6
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0962
  time to fit residues: 7.3729
Evaluate side-chains
  59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain I residue   28 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    2.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.123690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.093758 restraints weight = 5464.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.82
r_work: 0.3197 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4975  Z= 0.154
  Angle     :  0.441   5.839   6720  Z= 0.243
  Chirality :  0.050   0.127    870
  Planarity :  0.001   0.005    845
  Dihedral  :  4.736  15.150    725
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.35 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.40 (0.27), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR E  39 
 PHE   0.011   0.002   PHE F  94 
 HIS   0.005   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4975)
  covalent geometry    : angle       0.44057 ( 6720)
  hydrogen bonds       : bond        0.01280 (   79)
  hydrogen bonds       : angle       4.06620 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.171 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7882 (mp)
REVERT: B   97 LYS cc_start: 0.8556 (mttt) cc_final: 0.8255 (mttt)
REVERT: C   35 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7008 (pt0)
REVERT: E   32 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8288 (ttmm)
REVERT: G   43 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7116 (mttt)
REVERT: I   28 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7747 (mt-10)
REVERT: J   60 LYS cc_start: 0.8993 (mppt) cc_final: 0.8697 (mptt)
  outliers start: 11
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0911
  time to fit residues: 7.3513
Evaluate side-chains
  65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.122387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.092444 restraints weight = 5557.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.82
r_work: 0.3173 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4975  Z= 0.212
  Angle     :  0.479   6.921   6720  Z= 0.262
  Chirality :  0.050   0.126    870
  Planarity :  0.001   0.006    845
  Dihedral  :  4.874  15.470    725
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.12 %
    Favored  : 80.82 %
  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: -3.37 (0.27), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR E  39 
 PHE   0.013   0.002   PHE F  94 
 HIS   0.006   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 4975)
  covalent geometry    : angle       0.47909 ( 6720)
  hydrogen bonds       : bond        0.01469 (   79)
  hydrogen bonds       : angle       4.14648 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.177 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: B   97 LYS cc_start: 0.8548 (mttt) cc_final: 0.8242 (mttt)
REVERT: C   35 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8425 (mm-30)
REVERT: E   28 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7548 (mt-10)
REVERT: E   32 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8234 (ttmm)
REVERT: G   43 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7086 (mttt)
REVERT: I   28 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7745 (mt-10)
REVERT: J   60 LYS cc_start: 0.9024 (mppt) cc_final: 0.8077 (mptt)
  outliers start: 15
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0906
  time to fit residues: 7.2360
Evaluate side-chains
  70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   28 GLU
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.122288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.092502 restraints weight = 5523.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.81
r_work: 0.3178 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4975  Z= 0.203
  Angle     :  0.471   6.866   6720  Z= 0.258
  Chirality :  0.050   0.127    870
  Planarity :  0.001   0.006    845
  Dihedral  :  4.852  15.859    725
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.31 %
    Favored  : 80.82 %
  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: -3.34 (0.27), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR A  39 
 PHE   0.013   0.002   PHE F  94 
 HIS   0.005   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 4975)
  covalent geometry    : angle       0.47143 ( 6720)
  hydrogen bonds       : bond        0.01417 (   79)
  hydrogen bonds       : angle       4.12405 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.179 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7925 (mp)
REVERT: B   97 LYS cc_start: 0.8607 (mttt) cc_final: 0.8297 (mttt)
REVERT: C   35 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: E   28 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7579 (mt-10)
REVERT: E   32 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8287 (ttmm)
REVERT: G   43 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7154 (mttt)
REVERT: I   28 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7799 (mt-10)
REVERT: J   60 LYS cc_start: 0.9048 (mppt) cc_final: 0.8101 (mptt)
  outliers start: 19
  outliers final: 15
  residues processed: 65
  average time/residue: 0.0890
  time to fit residues: 7.2119
Evaluate side-chains
  72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   28 GLU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    6.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.089589 restraints weight = 5673.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.79
r_work: 0.3183 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   4975  Z= 0.348
  Angle     :  0.566   7.093   6720  Z= 0.313
  Chirality :  0.052   0.125    870
  Planarity :  0.002   0.007    845
  Dihedral  :  5.218  15.904    725
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.51 %
    Favored  : 80.82 %
  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: -3.52 (0.26), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR A  39 
 PHE   0.016   0.003   PHE F  94 
 HIS   0.008   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00767 ( 4975)
  covalent geometry    : angle       0.56572 ( 6720)
  hydrogen bonds       : bond        0.01755 (   79)
  hydrogen bonds       : angle       4.38551 (  237)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.140 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7728 (mp)
REVERT: C   35 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8446 (mm-30)
REVERT: E   28 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7450 (mt-10)
REVERT: E   32 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8314 (ttmm)
REVERT: G   43 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7125 (mttt)
REVERT: I   28 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7718 (mt-10)
REVERT: J   60 LYS cc_start: 0.9060 (mppt) cc_final: 0.8175 (mptt)
  outliers start: 18
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0923
  time to fit residues: 8.1020
Evaluate side-chains
  77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   28 GLU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain F residue   97 LYS
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   28 GLU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.122851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.092906 restraints weight = 5591.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.83
r_work: 0.3240 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4975  Z= 0.184
  Angle     :  0.470   6.659   6720  Z= 0.256
  Chirality :  0.050   0.130    870
  Planarity :  0.001   0.006    845
  Dihedral  :  4.905  15.787    725
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.33 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.27), residues: 705
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.20), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR A  39 
 PHE   0.012   0.002   PHE F  94 
 HIS   0.005   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 4975)
  covalent geometry    : angle       0.46956 ( 6720)
  hydrogen bonds       : bond        0.01364 (   79)
  hydrogen bonds       : angle       4.12399 (  237)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1105.22 seconds
wall clock time: 19 minutes 42.15 seconds (1182.15 seconds total)