Starting phenix.real_space_refine
on Fri May  9 22:43:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qpz_18570/05_2025/8qpz_18570.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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    2520      2.51       5
     N     732      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4116
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 343
          Classifications: {'peptide': 51}
          Link IDs: {'TRANS': 50}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 1.70, per 1000 atoms: 0.41
  Number of scatterers: 4116
  At special positions: 0
  Unit cell: (82.65, 75.05, 46.55, 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     864      8.00
     N     732      7.00
     C    2520      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: 0.91
  Conformation dependent library (CDL) restraints added in 526.4 milliseconds
  

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1056

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 67.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 57
      removed outlier: 6.426A  pdb=" N   LYS A  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL C  48 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   GLY A  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 9.803A  pdb=" N   HIS C  50 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 8.864A  pdb=" N   VAL A  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 9.277A  pdb=" N   VAL C  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   GLY A  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   THR C  54 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   ALA C  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL E  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   VAL C  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   HIS E  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   GLY C  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL G  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL E  49 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   HIS G  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY E  51 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LYS G  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL I  48 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   GLY G  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 9.746A  pdb=" N   HIS I  50 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   VAL G  49 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 9.243A  pdb=" N   VAL I  52 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLY G  51 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   THR I  54 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ALA G  53 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ALA I  56 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   VAL G  55 " --> pdb=" O   ALA I  56 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL K  48 " --> pdb=" O   GLY I  47 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   VAL I  49 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   HIS K  50 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLY I  51 " --> pdb=" O   HIS K  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65
      removed outlier: 6.542A  pdb=" N   LYS A  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   VAL C  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLN A  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   ASN C  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   THR A  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LYS C  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   VAL E  63 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLN C  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   ASN E  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR C  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS E  60 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   VAL G  63 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   GLN E  62 " --> pdb=" O   VAL G  63 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ASN G  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   THR E  64 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LYS G  60 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   VAL I  63 " --> pdb=" O   LYS G  60 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLN G  62 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ASN I  65 " --> pdb=" O   GLN G  62 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   THR G  64 " --> pdb=" O   ASN I  65 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS I  60 " --> pdb=" O   GLU K  61 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   VAL K  63 " --> pdb=" O   LYS I  60 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN I  62 " --> pdb=" O   VAL K  63 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN K  65 " --> pdb=" O   GLN I  62 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR I  64 " --> pdb=" O   ASN K  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71
    Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 81
      removed outlier: 6.188A  pdb=" N   VAL A  74 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   VAL C  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   ALA A  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 9.949A  pdb=" N   GLN C  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 9.022A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 10.558A  pdb=" N   THR C  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 9.261A  pdb=" N   LYS A  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL C  74 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   VAL E  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   ALA C  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 9.867A  pdb=" N   GLN E  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.931A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 10.453A  pdb=" N   THR E  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 9.129A  pdb=" N   LYS C  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL E  74 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL G  77 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ALA E  76 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 9.780A  pdb=" N   GLN G  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.843A  pdb=" N   ALA E  78 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 10.363A  pdb=" N   THR G  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 9.029A  pdb=" N   LYS E  80 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL G  74 " --> pdb=" O   THR I  75 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   VAL I  77 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   ALA G  76 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 10.009A  pdb=" N   GLN I  79 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 9.080A  pdb=" N   ALA G  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 10.623A  pdb=" N   THR I  81 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 9.342A  pdb=" N   LYS G  80 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL I  74 " --> pdb=" O   THR K  75 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   VAL K  77 " --> pdb=" O   VAL I  74 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ALA I  76 " --> pdb=" O   VAL K  77 " (cutoff:3.500A)
      removed outlier: 9.827A  pdb=" N   GLN K  79 " --> pdb=" O   ALA I  76 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   ALA I  78 " --> pdb=" O   GLN K  79 " (cutoff:3.500A)
      removed outlier: 10.417A  pdb=" N   THR K  81 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 9.108A  pdb=" N   LYS I  80 " --> pdb=" O   THR K  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 57
      removed outlier: 6.831A  pdb=" N   VAL D  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL B  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   HIS D  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLY B  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL F  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   VAL D  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   HIS F  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   GLY D  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL H  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL F  49 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   HIS H  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   GLY F  51 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LYS H  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   VAL J  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   GLY H  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
      removed outlier: 9.908A  pdb=" N   HIS J  50 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 8.928A  pdb=" N   VAL H  49 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 9.326A  pdb=" N   VAL J  52 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLY H  51 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   THR J  54 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA H  53 " --> pdb=" O   THR J  54 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ALA J  56 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL H  55 " --> pdb=" O   ALA J  56 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 57
      removed outlier: 6.831A  pdb=" N   VAL D  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL B  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   HIS D  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLY B  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL F  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   VAL D  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   HIS F  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   GLY D  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL H  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL F  49 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   HIS H  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   GLY F  51 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LYS H  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   VAL J  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   GLY H  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
      removed outlier: 9.908A  pdb=" N   HIS J  50 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 8.928A  pdb=" N   VAL H  49 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 9.326A  pdb=" N   VAL J  52 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLY H  51 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   THR J  54 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA H  53 " --> pdb=" O   THR J  54 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ALA J  56 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL H  55 " --> pdb=" O   ALA J  56 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   HIS L  50 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   GLY J  51 " --> pdb=" O   HIS L  50 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL L  52 " --> pdb=" O   GLY J  51 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 65
      removed outlier: 6.582A  pdb=" N   LYS B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 8.251A  pdb=" N   VAL D  63 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   GLN B  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   ASN D  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   THR B  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LYS D  60 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 8.330A  pdb=" N   VAL F  63 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN D  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   ASN F  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   THR D  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LYS F  60 " --> pdb=" O   GLU H  61 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   VAL H  63 " --> pdb=" O   LYS F  60 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLN F  62 " --> pdb=" O   VAL H  63 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ASN H  65 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   THR F  64 " --> pdb=" O   ASN H  65 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LYS H  60 " --> pdb=" O   GLU J  61 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL J  63 " --> pdb=" O   LYS H  60 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN H  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ASN J  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   THR H  64 " --> pdb=" O   ASN J  65 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   LYS J  60 " --> pdb=" O   GLU L  61 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   VAL L  63 " --> pdb=" O   LYS J  60 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN J  62 " --> pdb=" O   VAL L  63 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ASN L  65 " --> pdb=" O   GLN J  62 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR J  64 " --> pdb=" O   ASN L  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 71
    Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 81
      removed outlier: 6.201A  pdb=" N   VAL B  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   VAL D  77 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ALA B  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 8.947A  pdb=" N   ALA B  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   THR D  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 9.155A  pdb=" N   LYS B  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL D  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL F  77 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   ALA D  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 9.922A  pdb=" N   GLN F  79 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   ALA D  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 10.512A  pdb=" N   THR F  81 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 9.191A  pdb=" N   LYS D  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL F  74 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   VAL H  77 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ALA F  76 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 9.834A  pdb=" N   GLN H  79 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   ALA F  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 10.442A  pdb=" N   THR H  81 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 9.131A  pdb=" N   LYS F  80 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   VAL H  74 " --> pdb=" O   THR J  75 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL J  77 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   ALA H  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
      removed outlier: 9.739A  pdb=" N   GLN J  79 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   ALA H  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   THR J  81 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   LYS H  80 " --> pdb=" O   THR J  81 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   VAL J  74 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   VAL L  77 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   ALA J  76 " --> pdb=" O   VAL L  77 " (cutoff:3.500A)
      removed outlier: 9.913A  pdb=" N   GLN L  79 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 8.992A  pdb=" N   ALA J  78 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 10.511A  pdb=" N   THR L  81 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 9.235A  pdb=" N   LYS J  80 " --> pdb=" O   THR L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 88

    129 hydrogen bonds defined for protein.
    387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 744
        1.29 -     1.35: 660
        1.35 -     1.42: 46
        1.42 -     1.48: 722
        1.48 -     1.54: 1944
  Bond restraints: 4116
  Sorted by residual:
  bond pdb=" CB  LYS K  80 "
       pdb=" CG  LYS K  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.94e-01
  bond pdb=" CB  LYS C  80 "
       pdb=" CG  LYS C  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.85e-01
  bond pdb=" CB  LYS J  80 "
       pdb=" CG  LYS J  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.85e-01
  bond pdb=" CB  LYS F  80 "
       pdb=" CG  LYS F  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.72e-01
  bond pdb=" CB  LYS D  80 "
       pdb=" CG  LYS D  80 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.66e-01
  ... (remaining 4111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 5017
        1.00 -     2.00: 443
        2.00 -     3.00: 84
        3.00 -     4.00: 1
        4.00 -     4.99: 35
  Bond angle restraints: 5580
  Sorted by residual:
  angle pdb=" N   GLY L  73 "
        pdb=" CA  GLY L  73 "
        pdb=" C   GLY L  73 "
      ideal   model   delta    sigma   weight residual
     113.76  118.75   -4.99 1.80e+00 3.09e-01 7.70e+00
  angle pdb=" N   GLY K  73 "
        pdb=" CA  GLY K  73 "
        pdb=" C   GLY K  73 "
      ideal   model   delta    sigma   weight residual
     113.76  118.75   -4.99 1.80e+00 3.09e-01 7.69e+00
  angle pdb=" N   GLY J  73 "
        pdb=" CA  GLY J  73 "
        pdb=" C   GLY J  73 "
      ideal   model   delta    sigma   weight residual
     113.76  118.74   -4.98 1.80e+00 3.09e-01 7.66e+00
  angle pdb=" N   GLY C  73 "
        pdb=" CA  GLY C  73 "
        pdb=" C   GLY C  73 "
      ideal   model   delta    sigma   weight residual
     113.76  118.74   -4.98 1.80e+00 3.09e-01 7.66e+00
  angle pdb=" N   GLY D  73 "
        pdb=" CA  GLY D  73 "
        pdb=" C   GLY D  73 "
      ideal   model   delta    sigma   weight residual
     113.76  118.74   -4.98 1.80e+00 3.09e-01 7.65e+00
  ... (remaining 5575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.24: 2160
        9.24 -    18.47: 168
       18.47 -    27.70: 60
       27.70 -    36.94: 12
       36.94 -    46.17: 36
  Dihedral angle restraints: 2436
    sinusoidal: 780
      harmonic: 1656
  Sorted by residual:
  dihedral pdb=" CA  LYS G  80 "
           pdb=" CB  LYS G  80 "
           pdb=" CG  LYS G  80 "
           pdb=" CD  LYS G  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -133.83  -46.17     3      1.50e+01 4.44e-03 8.29e+00
  dihedral pdb=" CA  LYS E  80 "
           pdb=" CB  LYS E  80 "
           pdb=" CG  LYS E  80 "
           pdb=" CD  LYS E  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -133.83  -46.17     3      1.50e+01 4.44e-03 8.29e+00
  dihedral pdb=" CA  LYS D  80 "
           pdb=" CB  LYS D  80 "
           pdb=" CG  LYS D  80 "
           pdb=" CD  LYS D  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -133.84  -46.16     3      1.50e+01 4.44e-03 8.29e+00
  ... (remaining 2433 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 361
       0.025 -    0.050: 242
       0.050 -    0.075: 33
       0.075 -    0.101: 72
       0.101 -    0.126: 60
  Chirality restraints: 768
  Sorted by residual:
  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   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  ILE H  88 "
            pdb=" N   ILE H  88 "
            pdb=" C   ILE H  88 "
            pdb=" CB  ILE H  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE E  88 "
            pdb=" N   ILE E  88 "
            pdb=" C   ILE E  88 "
            pdb=" CB  ILE E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 765 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  66 "    0.005 2.00e-02 2.50e+03   1.05e-02 1.10e+00
        pdb=" C   VAL A  66 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL A  66 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY A  67 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  66 "    0.005 2.00e-02 2.50e+03   1.05e-02 1.10e+00
        pdb=" C   VAL E  66 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL E  66 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY E  67 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL K  66 "    0.005 2.00e-02 2.50e+03   1.05e-02 1.09e+00
        pdb=" C   VAL K  66 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL K  66 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY K  67 "    0.006 2.00e-02 2.50e+03
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 2146
        2.98 -     3.46: 3347
        3.46 -     3.94: 6414
        3.94 -     4.42: 6543
        4.42 -     4.90: 13172
  Nonbonded interactions: 31622
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN H  79 "
            pdb=" OG1 THR H  81 "
     model   vdw
     2.495 3.040
  nonbonded pdb=" OE1 GLN B  79 "
            pdb=" OG1 THR B  81 "
     model   vdw
     2.496 3.040
  nonbonded pdb=" OE1 GLN I  79 "
            pdb=" OG1 THR I  81 "
     model   vdw
     2.496 3.040
  nonbonded pdb=" OE1 GLN E  79 "
            pdb=" OG1 THR E  81 "
     model   vdw
     2.496 3.040
  nonbonded pdb=" OE1 GLN A  79 "
            pdb=" OG1 THR A  81 "
     model   vdw
     2.496 3.040
  ... (remaining 31617 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

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:             1.730
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.060
  Process input model:                     12.590
  Find NCS groups from input model:        0.090
  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:11.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
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      :  0.004   0.023   4116  Z= 0.203
  Angle     :  0.696   4.994   5580  Z= 0.415
  Chirality :  0.049   0.126    768
  Planarity :  0.002   0.011    696
  Dihedral  : 10.844  46.171   1380
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  8.57 %
    Allowed  :  5.71 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.31), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.00 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS K  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24038 (  102)
  hydrogen bonds       : angle       7.49509 (  387)
  covalent geometry    : bond        0.00442 ( 4116)
  covalent geometry    : angle       0.69625 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 36
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6807 (mttt) cc_final: 0.5959 (mmmt)
REVERT: A   80 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6464 (ttpt)
REVERT: B   43 LYS cc_start: 0.6507 (mttt) cc_final: 0.5784 (mmmt)
REVERT: B   80 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6622 (ttpt)
REVERT: C   43 LYS cc_start: 0.6245 (mttt) cc_final: 0.6038 (mtpt)
REVERT: C   80 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7219 (mtpp)
REVERT: E   43 LYS cc_start: 0.6282 (mttt) cc_final: 0.6047 (mtpt)
REVERT: E   80 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6803 (tmtt)
REVERT: G   43 LYS cc_start: 0.6711 (mttt) cc_final: 0.6504 (mtpt)
REVERT: I   80 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7068 (tttm)
REVERT: K   43 LYS cc_start: 0.6558 (mttt) cc_final: 0.5306 (pmtt)
REVERT: K   46 GLU cc_start: 0.7212 (mt-10) cc_final: 0.5725 (mm-30)
REVERT: K   80 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6978 (tttp)
REVERT: L   43 LYS cc_start: 0.6437 (mttt) cc_final: 0.6219 (mtpt)
REVERT: L   46 GLU cc_start: 0.7234 (mt-10) cc_final: 0.5941 (tt0)
REVERT: L   80 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7047 (tttp)
  outliers start: 36
  outliers final: 27
  residues processed: 72
  average time/residue: 1.3820
  time to fit residues: 102.5388
Evaluate side-chains
  52 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 18
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   80 LYS
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 LYS
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   80 LYS
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
C  65 ASN
C  79 GLN
D  79 GLN
E  79 GLN
F  79 GLN
G  79 GLN
H  79 GLN
I  62 GLN
I  79 GLN
K  79 GLN
L  79 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.150670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.131057 restraints weight = 4929.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.4146 rms_B_bonded: 2.27
r_work: 0.4049 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3936 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   4116  Z= 0.338
  Angle     :  0.689   5.113   5580  Z= 0.414
  Chirality :  0.052   0.146    768
  Planarity :  0.003   0.010    696
  Dihedral  : 11.629  59.735    664
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers : 11.43 %
    Allowed  :  6.90 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.28), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.29 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06359 (  102)
  hydrogen bonds       : angle       5.54308 (  387)
  covalent geometry    : bond        0.00735 ( 4116)
  covalent geometry    : angle       0.68922 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 32
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6754 (mttt) cc_final: 0.6088 (mmmt)
REVERT: B   43 LYS cc_start: 0.6348 (mttt) cc_final: 0.5744 (mmmt)
REVERT: C   43 LYS cc_start: 0.6613 (mttt) cc_final: 0.6371 (mtpt)
REVERT: E   43 LYS cc_start: 0.6469 (mttt) cc_final: 0.6214 (mtpt)
REVERT: G   43 LYS cc_start: 0.6716 (mttt) cc_final: 0.6445 (mtpt)
REVERT: G   57 GLU cc_start: 0.8270 (tt0) cc_final: 0.7897 (mt-10)
REVERT: K   43 LYS cc_start: 0.6732 (mttt) cc_final: 0.5588 (pmtt)
REVERT: L   80 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7476 (mtpt)
  outliers start: 48
  outliers final: 42
  residues processed: 80
  average time/residue: 1.0757
  time to fit residues: 89.4079
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 25
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   82 VAL
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   80 LYS
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   43 LYS
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   82 VAL
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   80 LYS
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
J  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.154461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.133474 restraints weight = 4840.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4201 rms_B_bonded: 2.40
r_work: 0.4114 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4116  Z= 0.159
  Angle     :  0.499   3.479   5580  Z= 0.302
  Chirality :  0.048   0.138    768
  Planarity :  0.002   0.009    696
  Dihedral  :  8.439  58.427    640
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 13.57 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.29), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.29 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  102)
  hydrogen bonds       : angle       4.86286 (  387)
  covalent geometry    : bond        0.00333 ( 4116)
  covalent geometry    : angle       0.49944 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 26
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6744 (mttt) cc_final: 0.6214 (mmmt)
REVERT: B   43 LYS cc_start: 0.6523 (mttt) cc_final: 0.5912 (mmmt)
REVERT: E   43 LYS cc_start: 0.6416 (mttt) cc_final: 0.6177 (mtpt)
REVERT: G   43 LYS cc_start: 0.6750 (mttt) cc_final: 0.6466 (mtpt)
REVERT: G   57 GLU cc_start: 0.8235 (tt0) cc_final: 0.7898 (mt-10)
REVERT: K   43 LYS cc_start: 0.6789 (mttt) cc_final: 0.5658 (pmtt)
REVERT: L   80 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7515 (mtpt)
  outliers start: 24
  outliers final: 17
  residues processed: 50
  average time/residue: 1.3565
  time to fit residues: 70.1210
Evaluate side-chains
  40 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 22
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   80 LYS
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain L residue   80 LYS
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    4.1988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.150960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.130458 restraints weight = 5036.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 2.40
r_work: 0.4062 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3946 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   4116  Z= 0.240
  Angle     :  0.557   3.917   5580  Z= 0.336
  Chirality :  0.050   0.144    768
  Planarity :  0.002   0.010    696
  Dihedral  :  8.382  58.231    627
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  9.76 %
    Allowed  : 10.71 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.28), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04883 (  102)
  hydrogen bonds       : angle       4.92016 (  387)
  covalent geometry    : bond        0.00513 ( 4116)
  covalent geometry    : angle       0.55674 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 26
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6785 (mttt) cc_final: 0.6237 (mmmt)
REVERT: B   43 LYS cc_start: 0.6667 (mttt) cc_final: 0.6093 (mmmt)
REVERT: C   72 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8124 (m)
REVERT: E   43 LYS cc_start: 0.6346 (mttt) cc_final: 0.6111 (mtpt)
REVERT: G   43 LYS cc_start: 0.6666 (mttt) cc_final: 0.6408 (mtpt)
REVERT: G   57 GLU cc_start: 0.8265 (tt0) cc_final: 0.7888 (mt-10)
REVERT: J   72 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8003 (m)
REVERT: K   43 LYS cc_start: 0.6838 (mttt) cc_final: 0.5670 (pmtt)
REVERT: L   80 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7663 (mtpt)
  outliers start: 41
  outliers final: 34
  residues processed: 67
  average time/residue: 0.9472
  time to fit residues: 66.3594
Evaluate side-chains
  62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 25
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   82 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain I residue   43 LYS
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   82 VAL
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   80 LYS
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.155235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.135196 restraints weight = 4848.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.4209 rms_B_bonded: 2.32
r_work: 0.4117 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4003 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   4116  Z= 0.124
  Angle     :  0.456   4.037   5580  Z= 0.276
  Chirality :  0.048   0.138    768
  Planarity :  0.002   0.009    696
  Dihedral  :  7.250  56.574    626
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 14.29 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.29), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  102)
  hydrogen bonds       : angle       4.56193 (  387)
  covalent geometry    : bond        0.00257 ( 4116)
  covalent geometry    : angle       0.45601 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 31
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6752 (mttt) cc_final: 0.6219 (mmmt)
REVERT: B   43 LYS cc_start: 0.6715 (mttt) cc_final: 0.6063 (mmmt)
REVERT: E   43 LYS cc_start: 0.6328 (mttt) cc_final: 0.6098 (mtpt)
REVERT: G   43 LYS cc_start: 0.6142 (mttt) cc_final: 0.5892 (mtpt)
REVERT: G   57 GLU cc_start: 0.8135 (tt0) cc_final: 0.7834 (mt-10)
REVERT: K   43 LYS cc_start: 0.6781 (mttt) cc_final: 0.5617 (pmtt)
REVERT: L   80 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7629 (mtpt)
  outliers start: 22
  outliers final: 15
  residues processed: 53
  average time/residue: 1.2624
  time to fit residues: 69.3035
Evaluate side-chains
  44 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 28
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain L residue   80 LYS
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.149334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.128889 restraints weight = 5065.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 2.37
r_work: 0.4043 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   4116  Z= 0.322
  Angle     :  0.618   3.831   5580  Z= 0.372
  Chirality :  0.053   0.147    768
  Planarity :  0.003   0.010    696
  Dihedral  :  7.489  58.695    618
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers : 10.24 %
    Allowed  :  9.05 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.28), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.21), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05438 (  102)
  hydrogen bonds       : angle       4.86870 (  387)
  covalent geometry    : bond        0.00686 ( 4116)
  covalent geometry    : angle       0.61808 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 27
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6820 (mttt) cc_final: 0.6208 (mmmt)
REVERT: B   43 LYS cc_start: 0.6820 (mttt) cc_final: 0.6175 (mmmt)
REVERT: C   72 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8154 (m)
REVERT: E   43 LYS cc_start: 0.6290 (mttt) cc_final: 0.6089 (mtpt)
REVERT: G   43 LYS cc_start: 0.6234 (mttt) cc_final: 0.5952 (mtpt)
REVERT: G   57 GLU cc_start: 0.8259 (tt0) cc_final: 0.7881 (mt-10)
REVERT: K   43 LYS cc_start: 0.6897 (mttt) cc_final: 0.5783 (pmtt)
  outliers start: 43
  outliers final: 36
  residues processed: 70
  average time/residue: 0.8579
  time to fit residues: 62.9930
Evaluate side-chains
  63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 26
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   82 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   82 VAL
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.4390 r_free = 0.4390 target = 0.154749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.134500 restraints weight = 4786.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 2.34
r_work: 0.4105 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3989 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   4116  Z= 0.133
  Angle     :  0.462   3.009   5580  Z= 0.281
  Chirality :  0.048   0.140    768
  Planarity :  0.002   0.011    696
  Dihedral  :  6.688  53.829    614
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 11.67 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.30), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  102)
  hydrogen bonds       : angle       4.52740 (  387)
  covalent geometry    : bond        0.00276 ( 4116)
  covalent geometry    : angle       0.46185 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 32
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6800 (mttt) cc_final: 0.6194 (mmmt)
REVERT: B   43 LYS cc_start: 0.6763 (mttt) cc_final: 0.6141 (mmmt)
REVERT: E   43 LYS cc_start: 0.6410 (mttt) cc_final: 0.6194 (mtpt)
REVERT: G   43 LYS cc_start: 0.6161 (mttt) cc_final: 0.5907 (mtpt)
REVERT: G   57 GLU cc_start: 0.8135 (tt0) cc_final: 0.7810 (mt-10)
REVERT: K   43 LYS cc_start: 0.6820 (mttt) cc_final: 0.5591 (pmtt)
  outliers start: 32
  outliers final: 28
  residues processed: 64
  average time/residue: 0.9732
  time to fit residues: 65.0661
Evaluate side-chains
  57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 29
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.4342 r_free = 0.4342 target = 0.150398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.129211 restraints weight = 4958.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.43
r_work: 0.4050 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3933 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   4116  Z= 0.302
  Angle     :  0.595   3.447   5580  Z= 0.360
  Chirality :  0.052   0.146    768
  Planarity :  0.003   0.011    696
  Dihedral  :  7.119  52.045    614
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  9.76 %
    Allowed  :  9.52 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.28), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05301 (  102)
  hydrogen bonds       : angle       4.78025 (  387)
  covalent geometry    : bond        0.00643 ( 4116)
  covalent geometry    : angle       0.59529 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 27
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6787 (mttt) cc_final: 0.6221 (mmmt)
REVERT: B   43 LYS cc_start: 0.6871 (mttt) cc_final: 0.6266 (mmmt)
REVERT: B   80 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7708 (mtpp)
REVERT: C   72 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (m)
REVERT: E   43 LYS cc_start: 0.6229 (mttt) cc_final: 0.5968 (mtpt)
REVERT: G   43 LYS cc_start: 0.6238 (mttt) cc_final: 0.5944 (mtpt)
REVERT: G   57 GLU cc_start: 0.8259 (tt0) cc_final: 0.7844 (mt-10)
REVERT: K   43 LYS cc_start: 0.6955 (mttt) cc_final: 0.5572 (pmtt)
  outliers start: 41
  outliers final: 35
  residues processed: 68
  average time/residue: 0.8628
  time to fit residues: 61.7785
Evaluate side-chains
  63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 26
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   82 VAL
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   82 VAL
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.4384 r_free = 0.4384 target = 0.154293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.133874 restraints weight = 4778.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 2.34
r_work: 0.4101 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4116  Z= 0.157
  Angle     :  0.481   2.779   5580  Z= 0.293
  Chirality :  0.049   0.142    768
  Planarity :  0.002   0.011    696
  Dihedral  :  6.688  52.789    614
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 11.67 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.30), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  102)
  hydrogen bonds       : angle       4.54728 (  387)
  covalent geometry    : bond        0.00328 ( 4116)
  covalent geometry    : angle       0.48093 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 30
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6801 (mttt) cc_final: 0.6231 (mmmt)
REVERT: B   43 LYS cc_start: 0.6839 (mttt) cc_final: 0.6259 (mmmt)
REVERT: E   43 LYS cc_start: 0.6288 (mttt) cc_final: 0.6013 (mtpt)
REVERT: G   43 LYS cc_start: 0.6220 (mttt) cc_final: 0.5959 (mtpt)
REVERT: G   57 GLU cc_start: 0.8156 (tt0) cc_final: 0.7816 (mt-10)
REVERT: K   43 LYS cc_start: 0.6911 (mttt) cc_final: 0.5562 (pmtt)
  outliers start: 32
  outliers final: 31
  residues processed: 62
  average time/residue: 0.8698
  time to fit residues: 56.6544
Evaluate side-chains
  61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 30
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0770
   chunk 38 optimal weight:    6.9990
   overall best weight:    3.6146

-------------------------------------------------------------------------------
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 = 0.4371 r_free = 0.4371 target = 0.152533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.131319 restraints weight = 4918.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.42
r_work: 0.4074 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4116  Z= 0.209
  Angle     :  0.519   2.998   5580  Z= 0.316
  Chirality :  0.050   0.143    768
  Planarity :  0.002   0.011    696
  Dihedral  :  6.763  50.689    614
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  8.10 %
    Allowed  : 11.19 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.29), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04509 (  102)
  hydrogen bonds       : angle       4.63120 (  387)
  covalent geometry    : bond        0.00443 ( 4116)
  covalent geometry    : angle       0.51922 ( 5580)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 30
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6828 (mttt) cc_final: 0.6262 (mmmt)
REVERT: B   43 LYS cc_start: 0.6890 (mttt) cc_final: 0.6308 (mmmt)
REVERT: E   43 LYS cc_start: 0.6310 (mttt) cc_final: 0.6023 (mtpt)
REVERT: G   43 LYS cc_start: 0.6242 (mttt) cc_final: 0.5972 (mtpt)
REVERT: G   57 GLU cc_start: 0.8202 (tt0) cc_final: 0.7839 (mt-10)
REVERT: K   43 LYS cc_start: 0.6911 (mttt) cc_final: 0.5555 (pmtt)
  outliers start: 34
  outliers final: 32
  residues processed: 64
  average time/residue: 0.8914
  time to fit residues: 59.8625
Evaluate side-chains
  62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 30
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   80 LYS
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   80 LYS
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   87 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   80 LYS
Chi-restraints excluded: chain K residue   82 VAL
Chi-restraints excluded: chain K residue   87 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   81 THR
Chi-restraints excluded: chain L residue   82 VAL
Chi-restraints excluded: chain L residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
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 = 0.4360 r_free = 0.4360 target = 0.151599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.130339 restraints weight = 4897.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 2.42
r_work: 0.4057 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3941 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4116  Z= 0.257
  Angle     :  0.561   3.226   5580  Z= 0.341
  Chirality :  0.051   0.144    768
  Planarity :  0.003   0.011    696
  Dihedral  :  6.971  50.734    614
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  8.10 %
    Allowed  : 11.43 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.29), residues: 588
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.22), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS H  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05018 (  102)
  hydrogen bonds       : angle       4.70573 (  387)
  covalent geometry    : bond        0.00547 ( 4116)
  covalent geometry    : angle       0.56140 ( 5580)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3715.92 seconds
wall clock time: 64 minutes 51.07 seconds (3891.07 seconds total)