Starting phenix.real_space_refine
on Tue Mar  3 16:20:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l1t_0801/03_2026/6l1t_0801.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      10      5.16       5
     C    4360      2.51       5
     N    1210      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7010
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 701
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 99}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'PTR:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.67, per 1000 atoms: 0.10
  Number of scatterers: 7010
  At special positions: 0
  Unit cell: (194.743, 91.49, 50.973, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P      10     15.00
     O    1420      8.00
     N    1210      7.00
     C    4360      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: 0.68
  Conformation dependent library (CDL) restraints added in 343.1 milliseconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 25 sheets defined
      0.0% alpha, 45.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
      removed outlier: 6.243A  pdb=" N   PHE A   4 " --> pdb=" O   MET B   5 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   GLY B   7 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   LYS A   6 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   PHE B   4 " --> pdb=" O   MET C   5 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   GLY C   7 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LYS B   6 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   PHE C   4 " --> pdb=" O   MET D   5 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   GLY D   7 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LYS C   6 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   PHE D   4 " --> pdb=" O   MET E   5 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLY E   7 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS D   6 " --> pdb=" O   GLY E   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.921A  pdb=" N   LYS A  10 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LYS B  10 " --> pdb=" O   ALA C  11 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LYS C  10 " --> pdb=" O   ALA D  11 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LYS D  10 " --> pdb=" O   ALA E  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 16
      removed outlier: 6.639A  pdb=" N   VAL A  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL B  15 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL C  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ALA D  18 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL E  15 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL D  16 " --> pdb=" O   VAL E  15 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ALA E  17 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 28
      removed outlier: 6.938A  pdb=" N   VAL A  26 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL B  26 " --> pdb=" O   ALA C  27 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL C  26 " --> pdb=" O   ALA D  27 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL D  26 " --> pdb=" O   ALA E  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 36
      removed outlier: 5.387A  pdb=" N   GLU A  35 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   GLY B  31 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 10.595A  pdb=" N   LYS C  34 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      removed outlier: 9.255A  pdb=" N   THR B  33 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 9.330A  pdb=" N   GLY C  36 " --> pdb=" O   THR B  33 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   GLU B  35 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLY C  31 " --> pdb=" O   LYS D  32 " (cutoff:3.500A)
      removed outlier: 10.597A  pdb=" N   LYS D  34 " --> pdb=" O   GLY C  31 " (cutoff:3.500A)
      removed outlier: 9.246A  pdb=" N   THR C  33 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 9.328A  pdb=" N   GLY D  36 " --> pdb=" O   THR C  33 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   GLU C  35 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)
      removed outlier: 8.641A  pdb=" N   GLY D  31 " --> pdb=" O   LYS E  32 " (cutoff:3.500A)
      removed outlier: 10.310A  pdb=" N   LYS E  34 " --> pdb=" O   GLY D  31 " (cutoff:3.500A)
      removed outlier: 8.934A  pdb=" N   THR D  33 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 9.059A  pdb=" N   GLY E  36 " --> pdb=" O   THR D  33 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   GLU D  35 " --> pdb=" O   GLY E  36 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 40
      removed outlier: 6.269A  pdb=" N   PTR A  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   PTR B  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   PTR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   PTR D  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 43 through 45
      removed outlier: 6.588A  pdb=" N   LYS A  43 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS B  43 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LYS C  43 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LYS D  43 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.374A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL B  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL C  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL D  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 54
      removed outlier: 6.621A  pdb=" N   ALA A  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA B  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ALA C  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ALA D  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 70 through 82
      removed outlier: 6.949A  pdb=" N   VAL A  74 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   THR B  75 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ALA A  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL B  77 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA A  78 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   GLN B  79 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LYS A  80 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   THR B  81 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   VAL A  82 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL B  74 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR C  75 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ALA B  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL C  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA B  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLN C  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LYS B  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   THR C  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   VAL B  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL C  74 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR D  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA C  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL D  77 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA C  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLN D  79 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LYS C  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   THR D  81 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   VAL C  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL D  74 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 70 through 82
      removed outlier: 6.949A  pdb=" N   VAL A  74 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   THR B  75 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ALA A  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL B  77 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA A  78 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   GLN B  79 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LYS A  80 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   THR B  81 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   VAL A  82 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL B  74 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   THR C  75 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ALA B  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL C  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA B  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLN C  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LYS B  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   THR C  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   VAL B  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL C  74 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR D  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA C  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL D  77 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA C  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLN D  79 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LYS C  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   THR D  81 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   VAL C  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   ALA E  78 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL D  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS E  80 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLN D  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.341A  pdb=" N   VAL E  82 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   THR D  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 89 through 96
      removed outlier: 8.887A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 10.093A  pdb=" N   THR B  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   ALA A  91 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 10.089A  pdb=" N   PHE B  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   GLY A  93 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   LYS B  96 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 8.909A  pdb=" N   ALA B  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 10.121A  pdb=" N   THR C  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   ALA B  91 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 10.098A  pdb=" N   PHE C  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLY B  93 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 8.754A  pdb=" N   LYS C  96 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL B  95 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   ALA C  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 10.076A  pdb=" N   THR D  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   ALA C  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   PHE D  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   GLY C  93 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 8.712A  pdb=" N   LYS D  96 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL C  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   THR E  92 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 8.632A  pdb=" N   ALA D  91 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 9.844A  pdb=" N   PHE E  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLY D  93 " --> pdb=" O   PHE E  94 " (cutoff:3.500A)
      removed outlier: 8.559A  pdb=" N   LYS E  96 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL D  95 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 7
      removed outlier: 6.224A  pdb=" N   PHE F   4 " --> pdb=" O   MET G   5 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   GLY G   7 " --> pdb=" O   PHE F   4 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LYS F   6 " --> pdb=" O   GLY G   7 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   PHE G   4 " --> pdb=" O   MET H   5 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   GLY H   7 " --> pdb=" O   PHE G   4 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   LYS G   6 " --> pdb=" O   GLY H   7 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   PHE H   4 " --> pdb=" O   MET I   5 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   GLY I   7 " --> pdb=" O   PHE H   4 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS H   6 " --> pdb=" O   GLY I   7 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE I   4 " --> pdb=" O   MET J   5 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   GLY J   7 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   LYS I   6 " --> pdb=" O   GLY J   7 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 11
      removed outlier: 6.880A  pdb=" N   LYS F  10 " --> pdb=" O   ALA G  11 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LYS G  10 " --> pdb=" O   ALA H  11 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LYS H  10 " --> pdb=" O   ALA I  11 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LYS I  10 " --> pdb=" O   ALA J  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'F' and resid 14 through 16
      removed outlier: 6.713A  pdb=" N   VAL F  15 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL G  15 " --> pdb=" O   VAL H  16 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL H  15 " --> pdb=" O   VAL I  16 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   ALA I  18 " --> pdb=" O   VAL H  15 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ALA J  17 " --> pdb=" O   VAL I  16 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 28
      removed outlier: 7.025A  pdb=" N   VAL F  26 " --> pdb=" O   ALA G  27 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL G  26 " --> pdb=" O   ALA H  27 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL H  26 " --> pdb=" O   ALA I  27 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL I  26 " --> pdb=" O   ALA J  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'F' and resid 34 through 36
      removed outlier: 5.470A  pdb=" N   GLU F  35 " --> pdb=" O   GLY G  36 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   GLU G  35 " --> pdb=" O   GLY H  36 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   GLY H  31 " --> pdb=" O   LYS I  32 " (cutoff:3.500A)
      removed outlier: 10.650A  pdb=" N   LYS I  34 " --> pdb=" O   GLY H  31 " (cutoff:3.500A)
      removed outlier: 9.322A  pdb=" N   THR H  33 " --> pdb=" O   LYS I  34 " (cutoff:3.500A)
      removed outlier: 9.389A  pdb=" N   GLY I  36 " --> pdb=" O   THR H  33 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLU H  35 " --> pdb=" O   GLY I  36 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LYS I  32 " --> pdb=" O   THR J  33 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   GLU J  35 " --> pdb=" O   LYS I  32 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   LYS I  34 " --> pdb=" O   GLU J  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'F' and resid 39 through 40
      removed outlier: 6.282A  pdb=" N   PTR F  39 " --> pdb=" O   VAL G  40 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   PTR G  39 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   PTR H  39 " --> pdb=" O   VAL I  40 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   PTR I  39 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'F' and resid 43 through 45
      removed outlier: 6.556A  pdb=" N   LYS F  43 " --> pdb=" O   THR G  44 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS G  43 " --> pdb=" O   THR H  44 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LYS H  43 " --> pdb=" O   THR I  44 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LYS I  43 " --> pdb=" O   THR J  44 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 49
      removed outlier: 6.402A  pdb=" N   VAL F  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL G  48 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL H  48 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL I  48 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'F' and resid 52 through 54
      removed outlier: 6.686A  pdb=" N   ALA F  53 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ALA G  53 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA H  53 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 70 through 82
      removed outlier: 7.039A  pdb=" N   VAL F  74 " --> pdb=" O   GLY G  73 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   THR G  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA F  76 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL G  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA F  78 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   GLN G  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LYS F  80 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   THR G  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   VAL F  82 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL G  74 " --> pdb=" O   GLY H  73 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   THR H  75 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA G  76 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL H  77 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA G  78 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN H  79 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LYS G  80 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   THR H  81 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL G  82 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL H  74 " --> pdb=" O   GLY I  73 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL I  74 " --> pdb=" O   GLY J  73 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 70 through 82
      removed outlier: 7.039A  pdb=" N   VAL F  74 " --> pdb=" O   GLY G  73 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   THR G  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA F  76 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL G  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA F  78 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   GLN G  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LYS F  80 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   THR G  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   VAL F  82 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL G  74 " --> pdb=" O   GLY H  73 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   THR H  75 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA G  76 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL H  77 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA G  78 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN H  79 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LYS G  80 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   THR H  81 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL G  82 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   ALA I  78 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL H  77 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   LYS I  80 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   GLN H  79 " --> pdb=" O   LYS I  80 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   VAL I  82 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   THR H  81 " --> pdb=" O   VAL I  82 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   VAL I  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   LYS J  80 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   GLN I  79 " --> pdb=" O   LYS J  80 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   VAL J  82 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   THR I  81 " --> pdb=" O   VAL J  82 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 89 through 92
      removed outlier: 6.703A  pdb=" N   ALA F  90 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   GLY G  93 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 9.086A  pdb=" N   THR F  92 " --> pdb=" O   GLY G  93 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   VAL G  95 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL F  95 " --> pdb=" O   LYS G  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'F' and resid 89 through 92
      removed outlier: 6.703A  pdb=" N   ALA F  90 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   GLY G  93 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 9.086A  pdb=" N   THR F  92 " --> pdb=" O   GLY G  93 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   VAL G  95 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 8.832A  pdb=" N   ALA G  89 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 10.055A  pdb=" N   THR H  92 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   ALA G  91 " --> pdb=" O   THR H  92 " (cutoff:3.500A)
      removed outlier: 10.032A  pdb=" N   PHE H  94 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLY G  93 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   LYS H  96 " --> pdb=" O   GLY G  93 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL G  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   ALA H  89 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
      removed outlier: 10.173A  pdb=" N   THR I  92 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   ALA H  91 " --> pdb=" O   THR I  92 " (cutoff:3.500A)
      removed outlier: 10.154A  pdb=" N   PHE I  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLY H  93 " --> pdb=" O   PHE I  94 " (cutoff:3.500A)
      removed outlier: 8.818A  pdb=" N   LYS I  96 " --> pdb=" O   GLY H  93 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL H  95 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   ALA I  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
      removed outlier: 10.496A  pdb=" N   THR J  92 " --> pdb=" O   ALA I  89 " (cutoff:3.500A)
      removed outlier: 9.206A  pdb=" N   ALA I  91 " --> pdb=" O   THR J  92 " (cutoff:3.500A)
      removed outlier: 10.422A  pdb=" N   PHE J  94 " --> pdb=" O   ALA I  91 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLY I  93 " --> pdb=" O   PHE J  94 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   LYS J  96 " --> pdb=" O   GLY I  93 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL I  95 " --> pdb=" O   LYS J  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7

    43 hydrogen bonds defined for protein.
    129 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2320
        1.33 -     1.45: 517
        1.45 -     1.57: 4173
        1.57 -     1.68: 10
        1.68 -     1.80: 20
  Bond restraints: 7040
  Sorted by residual:
  bond pdb=" OH  PTR G  39 "
       pdb=" P   PTR G  39 "
    ideal  model  delta    sigma   weight residual
    1.769  1.604  0.165 2.00e-02 2.50e+03 6.77e+01
  bond pdb=" OH  PTR J  39 "
       pdb=" P   PTR J  39 "
    ideal  model  delta    sigma   weight residual
    1.769  1.604  0.165 2.00e-02 2.50e+03 6.77e+01
  bond pdb=" OH  PTR B  39 "
       pdb=" P   PTR B  39 "
    ideal  model  delta    sigma   weight residual
    1.769  1.605  0.164 2.00e-02 2.50e+03 6.76e+01
  bond pdb=" OH  PTR E  39 "
       pdb=" P   PTR E  39 "
    ideal  model  delta    sigma   weight residual
    1.769  1.605  0.164 2.00e-02 2.50e+03 6.76e+01
  bond pdb=" OH  PTR D  39 "
       pdb=" P   PTR D  39 "
    ideal  model  delta    sigma   weight residual
    1.769  1.605  0.164 2.00e-02 2.50e+03 6.76e+01
  ... (remaining 7035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 9111
        1.96 -     3.92: 289
        3.92 -     5.88: 46
        5.88 -     7.83: 14
        7.83 -     9.79: 10
  Bond angle restraints: 9470
  Sorted by residual:
  angle pdb=" OH  PTR G  39 "
        pdb=" P   PTR G  39 "
        pdb=" O2P PTR G  39 "
      ideal   model   delta    sigma   weight residual
      99.92  109.71   -9.79 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" OH  PTR F  39 "
        pdb=" P   PTR F  39 "
        pdb=" O2P PTR F  39 "
      ideal   model   delta    sigma   weight residual
      99.92  109.71   -9.79 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" OH  PTR A  39 "
        pdb=" P   PTR A  39 "
        pdb=" O2P PTR A  39 "
      ideal   model   delta    sigma   weight residual
      99.92  109.71   -9.79 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" OH  PTR D  39 "
        pdb=" P   PTR D  39 "
        pdb=" O2P PTR D  39 "
      ideal   model   delta    sigma   weight residual
      99.92  109.71   -9.79 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" OH  PTR C  39 "
        pdb=" P   PTR C  39 "
        pdb=" O2P PTR C  39 "
      ideal   model   delta    sigma   weight residual
      99.92  109.69   -9.77 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 9465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.61: 3650
       12.61 -    25.22: 430
       25.22 -    37.83: 120
       37.83 -    50.44: 50
       50.44 -    63.05: 30
  Dihedral angle restraints: 4280
    sinusoidal: 1570
      harmonic: 2710
  Sorted by residual:
  dihedral pdb=" CA  VAL B  49 "
           pdb=" C   VAL B  49 "
           pdb=" N   HIS B  50 "
           pdb=" CA  HIS B  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.15  -18.85     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  VAL G  49 "
           pdb=" C   VAL G  49 "
           pdb=" N   HIS G  50 "
           pdb=" CA  HIS G  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  VAL F  49 "
           pdb=" C   VAL F  49 "
           pdb=" N   HIS F  50 "
           pdb=" CA  HIS F  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.17  -18.83     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 568
       0.035 -    0.071: 358
       0.071 -    0.106: 132
       0.106 -    0.142: 90
       0.142 -    0.177: 32
  Chirality restraints: 1180
  Sorted by residual:
  chirality pdb=" CB  VAL B  55 "
            pdb=" CA  VAL B  55 "
            pdb=" CG1 VAL B  55 "
            pdb=" CG2 VAL B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CB  VAL J  55 "
            pdb=" CA  VAL J  55 "
            pdb=" CG1 VAL J  55 "
            pdb=" CG2 VAL J  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.84e-01
  chirality pdb=" CB  VAL A  55 "
            pdb=" CA  VAL A  55 "
            pdb=" CG1 VAL A  55 "
            pdb=" CG2 VAL A  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.77e-01
  ... (remaining 1177 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "   -0.010 2.00e-02 2.50e+03   8.68e-03 1.32e+00
        pdb=" CG  PHE B  94 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  94 "    0.010 2.00e-02 2.50e+03   8.57e-03 1.29e+00
        pdb=" CG  PHE F  94 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  94 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  94 "    0.010 2.00e-02 2.50e+03   8.52e-03 1.27e+00
        pdb=" CG  PHE H  94 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  94 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  94 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2157
        2.82 -     3.34: 5891
        3.34 -     3.86: 10524
        3.86 -     4.38: 11308
        4.38 -     4.90: 22247
  Nonbonded interactions: 52127
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  34 "
            pdb=" O2P PTR E  39 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NZ  LYS G  34 "
            pdb=" O1P PTR G  39 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NZ  LYS D  34 "
            pdb=" O1P PTR D  39 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NZ  LYS E  34 "
            pdb=" O1P PTR E  39 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NZ  LYS F  34 "
            pdb=" O1P PTR F  39 "
     model   vdw
     2.314 3.120
  ... (remaining 52122 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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      :  0.011   0.165   7040  Z= 0.528
  Angle     :  0.928   9.793   9470  Z= 0.440
  Chirality :  0.060   0.177   1180
  Planarity :  0.002   0.009   1180
  Dihedral  : 14.396  63.051   2560
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.63 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.37 (0.15), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.11), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.020   0.003   PHE B  94 
 HIS   0.006   0.004   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01133 ( 7040)
  covalent geometry    : angle       0.92767 ( 9470)
  hydrogen bonds       : bond        0.30207 (   28)
  hydrogen bonds       : angle       8.94177 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 SER cc_start: 0.9172 (p) cc_final: 0.8949 (p)
REVERT: E   32 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8281 (mtpp)
REVERT: G   32 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8520 (mtpp)
REVERT: G   59 THR cc_start: 0.9161 (p) cc_final: 0.8923 (p)
REVERT: I    2 ASP cc_start: 0.8725 (p0) cc_final: 0.8415 (p0)
REVERT: J   57 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7065 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0590
  time to fit residues: 16.0389
Evaluate side-chains
  149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.120287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106737 restraints weight = 10884.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.77
r_work: 0.3525 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7040  Z= 0.140
  Angle     :  0.605   7.046   9470  Z= 0.316
  Chirality :  0.050   0.162   1180
  Planarity :  0.002   0.015   1180
  Dihedral  :  8.588  49.352   1100
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.53 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.60 (0.18), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.14), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.002   PHE E   4 
 HIS   0.001   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7040)
  covalent geometry    : angle       0.60524 ( 9470)
  hydrogen bonds       : bond        0.04074 (   28)
  hydrogen bonds       : angle       4.98046 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 193
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8025 (tp30) cc_final: 0.7815 (tm-30)
REVERT: A   42 SER cc_start: 0.9170 (p) cc_final: 0.8935 (p)
REVERT: C   13 GLU cc_start: 0.8185 (tp30) cc_final: 0.7932 (tp30)
REVERT: D    2 ASP cc_start: 0.8885 (p0) cc_final: 0.8547 (p0)
REVERT: D    8 LEU cc_start: 0.9213 (mm) cc_final: 0.8814 (mm)
REVERT: E   32 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8533 (mtpt)
REVERT: E   57 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7648 (mm-30)
REVERT: E   83 GLU cc_start: 0.7558 (mp0) cc_final: 0.7201 (mp0)
REVERT: G   13 GLU cc_start: 0.8249 (tp30) cc_final: 0.7102 (tp30)
REVERT: G   32 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8595 (mtpt)
REVERT: G   83 GLU cc_start: 0.7606 (mp0) cc_final: 0.7378 (mp0)
REVERT: H    2 ASP cc_start: 0.8702 (p0) cc_final: 0.8402 (p0)
REVERT: H   28 GLU cc_start: 0.7967 (tt0) cc_final: 0.7683 (mt-10)
REVERT: J    2 ASP cc_start: 0.8584 (p0) cc_final: 0.8348 (p0)
  outliers start: 34
  outliers final: 26
  residues processed: 211
  average time/residue: 0.0499
  time to fit residues: 15.8422
Evaluate side-chains
  204 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.0670
   chunk 9 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0270
   chunk 70 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    4.4182

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.111353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097988 restraints weight = 10923.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.72
r_work: 0.3383 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052   7040  Z= 0.374
  Angle     :  0.780   8.916   9470  Z= 0.410
  Chirality :  0.056   0.141   1180
  Planarity :  0.003   0.017   1180
  Dihedral  :  9.125  43.736   1100
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.95 %
    Favored  : 87.05 %
  Rotamer:
    Outliers : 10.44 %
    Allowed  : 16.32 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.55 (0.18), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.13), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.023   0.004   PHE G  94 
 HIS   0.006   0.003   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00848 ( 7040)
  covalent geometry    : angle       0.77953 ( 9470)
  hydrogen bonds       : bond        0.04515 (   28)
  hydrogen bonds       : angle       4.91104 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 170
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   42 SER cc_start: 0.9157 (p) cc_final: 0.8939 (p)
REVERT: B   32 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8841 (mtpp)
REVERT: D    2 ASP cc_start: 0.8923 (p0) cc_final: 0.8552 (p0)
REVERT: E   32 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8738 (mtpt)
REVERT: G   32 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8724 (mtpt)
REVERT: H    2 ASP cc_start: 0.8857 (p0) cc_final: 0.8512 (p0)
REVERT: J    2 ASP cc_start: 0.8915 (p0) cc_final: 0.8686 (p0)
  outliers start: 71
  outliers final: 65
  residues processed: 217
  average time/residue: 0.0526
  time to fit residues: 17.5131
Evaluate side-chains
  226 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 161
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue    8 LEU
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0010
   chunk 81 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.1992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.116036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.101801 restraints weight = 10899.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.82
r_work: 0.3453 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7040  Z= 0.198
  Angle     :  0.665   8.648   9470  Z= 0.344
  Chirality :  0.051   0.136   1180
  Planarity :  0.002   0.014   1180
  Dihedral  :  8.471  47.931   1100
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers : 10.88 %
    Allowed  : 16.47 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.25 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.14), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE I  94 
 HIS   0.003   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 7040)
  covalent geometry    : angle       0.66516 ( 9470)
  hydrogen bonds       : bond        0.03443 (   28)
  hydrogen bonds       : angle       4.59285 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 178
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.7596 (tp30) cc_final: 0.7344 (tm-30)
REVERT: A   42 SER cc_start: 0.9230 (p) cc_final: 0.9030 (p)
REVERT: B   13 GLU cc_start: 0.8157 (tp30) cc_final: 0.7351 (tp30)
REVERT: B   32 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8709 (mtpp)
REVERT: D    2 ASP cc_start: 0.8896 (p0) cc_final: 0.8499 (p0)
REVERT: D    8 LEU cc_start: 0.9191 (mm) cc_final: 0.8836 (mm)
REVERT: E   26 VAL cc_start: 0.9270 (m) cc_final: 0.8973 (t)
REVERT: E   32 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8583 (mtpt)
REVERT: G   32 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8707 (mtpt)
REVERT: H    2 ASP cc_start: 0.8695 (p0) cc_final: 0.8253 (p0)
REVERT: J    2 ASP cc_start: 0.8882 (p0) cc_final: 0.8645 (p0)
  outliers start: 74
  outliers final: 67
  residues processed: 225
  average time/residue: 0.0526
  time to fit residues: 18.0990
Evaluate side-chains
  239 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 172
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain I residue  100 LEU
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    0.1980
   chunk 94 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0870
   chunk 33 optimal weight:    4.9990
   chunk 88 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0570
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.0278

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.121149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.107030 restraints weight = 10746.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.81
r_work: 0.3552 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7040  Z= 0.114
  Angle     :  0.580   7.170   9470  Z= 0.300
  Chirality :  0.049   0.141   1180
  Planarity :  0.002   0.013   1180
  Dihedral  :  7.854  50.133   1100
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  9.56 %
    Allowed  : 17.50 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE C  94 
 HIS   0.001   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7040)
  covalent geometry    : angle       0.57993 ( 9470)
  hydrogen bonds       : bond        0.02624 (   28)
  hydrogen bonds       : angle       4.26526 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 190
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLU cc_start: 0.8052 (tp30) cc_final: 0.7128 (tp30)
REVERT: D    2 ASP cc_start: 0.8828 (p0) cc_final: 0.8393 (p0)
REVERT: D    8 LEU cc_start: 0.9135 (mm) cc_final: 0.8763 (mm)
REVERT: D   54 THR cc_start: 0.8956 (p) cc_final: 0.8579 (t)
REVERT: E   32 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8579 (mtpt)
REVERT: G   32 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8579 (mtpp)
REVERT: J    2 ASP cc_start: 0.8792 (p0) cc_final: 0.8521 (p0)
  outliers start: 65
  outliers final: 55
  residues processed: 228
  average time/residue: 0.0526
  time to fit residues: 18.3303
Evaluate side-chains
  241 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 186
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain I residue  100 LEU
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 87 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.116434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.102196 restraints weight = 10852.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.82
r_work: 0.3469 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7040  Z= 0.181
  Angle     :  0.647   8.411   9470  Z= 0.332
  Chirality :  0.050   0.134   1180
  Planarity :  0.002   0.012   1180
  Dihedral  :  8.024  47.778   1100
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers : 10.88 %
    Allowed  : 16.91 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.93 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE G  94 
 HIS   0.003   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7040)
  covalent geometry    : angle       0.64656 ( 9470)
  hydrogen bonds       : bond        0.03116 (   28)
  hydrogen bonds       : angle       4.39068 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 181
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: B   13 GLU cc_start: 0.8054 (tp30) cc_final: 0.7039 (tp30)
REVERT: B   32 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8701 (mtpp)
REVERT: D    2 ASP cc_start: 0.8809 (p0) cc_final: 0.8360 (p0)
REVERT: D    8 LEU cc_start: 0.9204 (mm) cc_final: 0.8833 (mm)
REVERT: D   54 THR cc_start: 0.8951 (p) cc_final: 0.8564 (t)
REVERT: E   32 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8546 (mtpt)
REVERT: J    2 ASP cc_start: 0.8823 (p0) cc_final: 0.8569 (p0)
  outliers start: 74
  outliers final: 69
  residues processed: 228
  average time/residue: 0.0502
  time to fit residues: 17.5056
Evaluate side-chains
  247 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 178
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain I residue  100 LEU
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 23 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0970
   chunk 51 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.9184

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.114394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.100104 restraints weight = 10899.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.81
r_work: 0.3434 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7040  Z= 0.253
  Angle     :  0.707   8.597   9470  Z= 0.366
  Chirality :  0.052   0.132   1180
  Planarity :  0.002   0.015   1180
  Dihedral  :  8.319  45.640   1100
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers : 10.59 %
    Allowed  : 17.94 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.003   PHE G  94 
 HIS   0.005   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 7040)
  covalent geometry    : angle       0.70736 ( 9470)
  hydrogen bonds       : bond        0.03526 (   28)
  hydrogen bonds       : angle       4.53189 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 178
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7068 (tm-30)
REVERT: B   13 GLU cc_start: 0.7985 (tp30) cc_final: 0.6933 (tp30)
REVERT: B   32 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8706 (mtpp)
REVERT: D    2 ASP cc_start: 0.8739 (p0) cc_final: 0.8305 (p0)
REVERT: D    8 LEU cc_start: 0.9201 (mm) cc_final: 0.8828 (mm)
REVERT: E   26 VAL cc_start: 0.9293 (m) cc_final: 0.8923 (t)
REVERT: E   32 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8562 (mtpt)
  outliers start: 72
  outliers final: 72
  residues processed: 226
  average time/residue: 0.0492
  time to fit residues: 17.2109
Evaluate side-chains
  249 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 177
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   74 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.117471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.103108 restraints weight = 10813.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.82
r_work: 0.3489 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7040  Z= 0.158
  Angle     :  0.641   8.961   9470  Z= 0.328
  Chirality :  0.050   0.134   1180
  Planarity :  0.002   0.011   1180
  Dihedral  :  8.013  49.207   1100
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  9.71 %
    Allowed  : 18.68 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.86 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.002   PHE C  94 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7040)
  covalent geometry    : angle       0.64105 ( 9470)
  hydrogen bonds       : bond        0.03007 (   28)
  hydrogen bonds       : angle       4.34589 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 183
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8718 (mtpp)
REVERT: D    2 ASP cc_start: 0.8724 (p0) cc_final: 0.8303 (p0)
REVERT: D    8 LEU cc_start: 0.9205 (mm) cc_final: 0.8842 (mm)
REVERT: E   32 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8577 (mtpt)
REVERT: G   32 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8582 (mtpp)
  outliers start: 66
  outliers final: 66
  residues processed: 225
  average time/residue: 0.0507
  time to fit residues: 17.4615
Evaluate side-chains
  247 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 181
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   66 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   74 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0270
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    4.0046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097907 restraints weight = 11030.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.81
r_work: 0.3403 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   7040  Z= 0.338
  Angle     :  0.777   9.204   9470  Z= 0.402
  Chirality :  0.054   0.140   1180
  Planarity :  0.003   0.017   1180
  Dihedral  :  8.570  43.753   1100
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.68 %
    Favored  : 86.32 %
  Rotamer:
    Outliers : 11.18 %
    Allowed  : 17.79 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.99 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.023   0.004   PHE G  94 
 HIS   0.007   0.003   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00769 ( 7040)
  covalent geometry    : angle       0.77711 ( 9470)
  hydrogen bonds       : bond        0.03881 (   28)
  hydrogen bonds       : angle       4.59854 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 176
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: B   32 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8731 (mtpp)
REVERT: D    2 ASP cc_start: 0.8646 (p0) cc_final: 0.8221 (p0)
REVERT: E   26 VAL cc_start: 0.9307 (m) cc_final: 0.8960 (t)
REVERT: E   32 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8655 (mtpt)
  outliers start: 76
  outliers final: 73
  residues processed: 229
  average time/residue: 0.0484
  time to fit residues: 17.1126
Evaluate side-chains
  245 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 172
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   55 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue    8 LEU
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   74 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.0570
   chunk 82 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0770
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.1658

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.120544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.106407 restraints weight = 10505.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.71
r_work: 0.3533 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7040  Z= 0.128
  Angle     :  0.651   9.160   9470  Z= 0.330
  Chirality :  0.049   0.137   1180
  Planarity :  0.002   0.026   1180
  Dihedral  :  7.973  50.262   1100
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  9.71 %
    Allowed  : 18.97 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.002   PHE C  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7040)
  covalent geometry    : angle       0.65122 ( 9470)
  hydrogen bonds       : bond        0.02860 (   28)
  hydrogen bonds       : angle       4.28753 (  129)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 185
  time to evaluate  : 0.179 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8772 (mtpp)
REVERT: C   13 GLU cc_start: 0.8293 (tp30) cc_final: 0.8013 (tp30)
REVERT: D    2 ASP cc_start: 0.8669 (p0) cc_final: 0.8239 (p0)
REVERT: D    8 LEU cc_start: 0.9217 (mm) cc_final: 0.8857 (mm)
REVERT: E   32 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8662 (mtpt)
REVERT: G   28 GLU cc_start: 0.8443 (tt0) cc_final: 0.8184 (mt-10)
REVERT: G   32 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8663 (mtpp)
  outliers start: 66
  outliers final: 66
  residues processed: 226
  average time/residue: 0.0507
  time to fit residues: 17.5821
Evaluate side-chains
  247 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 181
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   22 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   66 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   66 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain H residue   22 THR
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   77 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue    5 MET
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   70 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue    8 LEU
Chi-restraints excluded: chain J residue   22 THR
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   71 VAL
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.116789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.102702 restraints weight = 10612.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.70
r_work: 0.3484 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7040  Z= 0.214
  Angle     :  0.691   8.312   9470  Z= 0.354
  Chirality :  0.051   0.133   1180
  Planarity :  0.002   0.018   1180
  Dihedral  :  8.148  47.290   1100
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.79 %
    Favored  : 88.21 %
  Rotamer:
    Outliers : 10.44 %
    Allowed  : 18.97 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.82 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.003   PHE B  94 
 HIS   0.003   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 7040)
  covalent geometry    : angle       0.69128 ( 9470)
  hydrogen bonds       : bond        0.03273 (   28)
  hydrogen bonds       : angle       4.43410 (  129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1528.94 seconds
wall clock time: 26 minutes 56.54 seconds (1616.54 seconds total)