Starting phenix.real_space_refine
on Wed Feb 12 01:54:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6l1t_0801/02_2025/6l1t_0801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6l1t_0801/02_2025/6l1t_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_0801/02_2025/6l1t_0801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6l1t_0801/02_2025/6l1t_0801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6l1t_0801/02_2025/6l1t_0801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6l1t_0801/02_2025/6l1t_0801.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.65, per 1000 atoms: 0.38
  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.41
  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: 1.91

  Time building geometry restraints manager: 1.85 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.950
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.510
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
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= 0.700
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.006   0.004   HIS I  50 
 PHE   0.020   0.003   PHE B  94 

*********************** 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  : 0.725 
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: 0.8416 (p0)
REVERT: J   57 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7065 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1412
  time to fit residues: 37.3057
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  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.115195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.101574 restraints weight = 10997.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.81
r_work: 0.3436 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7040  Z= 0.313
  Angle     :  0.668   7.407   9470  Z= 0.349
  Chirality :  0.052   0.153   1180
  Planarity :  0.002   0.015   1180
  Dihedral  :  8.895  47.058   1100
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 16.91 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.71 (0.17), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.13), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS C  50 
 PHE   0.016   0.003   PHE G  94 

*********************** 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
  234 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 187
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8031 (tp30) cc_final: 0.7745 (tm-30)
REVERT: A   42 SER cc_start: 0.9154 (p) cc_final: 0.8930 (p)
REVERT: C   13 GLU cc_start: 0.8224 (tp30) cc_final: 0.7971 (tp30)
REVERT: D    2 ASP cc_start: 0.8881 (p0) cc_final: 0.8557 (p0)
REVERT: D   38 LEU cc_start: 0.9451 (tt) cc_final: 0.9195 (tp)
REVERT: E   32 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8573 (mtpt)
REVERT: G   32 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8532 (mtpp)
REVERT: G   83 GLU cc_start: 0.7619 (mp0) cc_final: 0.7398 (mp0)
REVERT: H    2 ASP cc_start: 0.8756 (p0) cc_final: 0.8481 (p0)
REVERT: J    2 ASP cc_start: 0.8696 (p0) cc_final: 0.8467 (p0)
  outliers start: 47
  outliers final: 42
  residues processed: 214
  average time/residue: 0.1285
  time to fit residues: 40.2157
Evaluate side-chains
  210 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 168
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   54 THR
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   44 THR
Chi-restraints excluded: chain D residue   70 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   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 F residue   59 THR
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   54 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   70 VAL
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   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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
F  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.111623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.098264 restraints weight = 10937.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.72
r_work: 0.3392 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046   7040  Z= 0.556
  Angle     :  0.784   7.087   9470  Z= 0.412
  Chirality :  0.056   0.134   1180
  Planarity :  0.003   0.018   1180
  Dihedral  :  9.206  44.227   1100
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.37 %
    Favored  : 86.63 %
  Rotamer:
    Outliers : 11.18 %
    Allowed  : 15.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.62 (0.17), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.13), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B  50 
 PHE   0.022   0.004   PHE D  94 

*********************** 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
  240 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 164
  time to evaluate  : 0.774 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8847 (mtpp)
REVERT: C   13 GLU cc_start: 0.8455 (tp30) cc_final: 0.8248 (tp30)
REVERT: D    2 ASP cc_start: 0.8919 (p0) cc_final: 0.8553 (p0)
REVERT: E   26 VAL cc_start: 0.9384 (m) cc_final: 0.9097 (t)
REVERT: E   32 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8730 (mtpt)
REVERT: G   13 GLU cc_start: 0.8346 (tp30) cc_final: 0.7396 (tp30)
REVERT: G   32 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8722 (mtpt)
REVERT: H    2 ASP cc_start: 0.8859 (p0) cc_final: 0.8547 (p0)
REVERT: J    2 ASP cc_start: 0.8915 (p0) cc_final: 0.8685 (p0)
  outliers start: 76
  outliers final: 72
  residues processed: 214
  average time/residue: 0.1261
  time to fit residues: 39.8714
Evaluate side-chains
  230 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 158
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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 B residue   92 THR
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   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   44 THR
Chi-restraints excluded: chain D residue   55 VAL
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   55 VAL
Chi-restraints excluded: chain G residue   59 THR
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   74 VAL
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   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   74 VAL
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.116104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.101999 restraints weight = 10954.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.82
r_work: 0.3456 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7040  Z= 0.271
  Angle     :  0.641   6.894   9470  Z= 0.334
  Chirality :  0.050   0.135   1180
  Planarity :  0.002   0.014   1180
  Dihedral  :  8.470  48.716   1100
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers : 10.15 %
    Allowed  : 17.35 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.14), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  50 
 PHE   0.015   0.002   PHE I  94 

*********************** 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
  246 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 177
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B   13 GLU cc_start: 0.8156 (tp30) cc_final: 0.7949 (tp30)
REVERT: D    2 ASP cc_start: 0.8881 (p0) cc_final: 0.8498 (p0)
REVERT: D    8 LEU cc_start: 0.9206 (mm) cc_final: 0.8845 (mm)
REVERT: E   32 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8589 (mtpt)
REVERT: F   13 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7086 (tm-30)
REVERT: G   13 GLU cc_start: 0.8029 (tp30) cc_final: 0.6975 (tp30)
REVERT: G   32 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8700 (mtpt)
REVERT: H    2 ASP cc_start: 0.8831 (p0) cc_final: 0.8430 (p0)
REVERT: J    2 ASP cc_start: 0.8894 (p0) cc_final: 0.8653 (p0)
  outliers start: 69
  outliers final: 60
  residues processed: 221
  average time/residue: 0.1191
  time to fit residues: 39.3164
Evaluate side-chains
  232 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 172
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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   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   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   55 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   74 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   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   66 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   74 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   54 THR
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   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   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   77 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0770
   chunk 50 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 72 optimal weight:    0.6980
   chunk 69 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    2.7544

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.113901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.099752 restraints weight = 10820.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.81
r_work: 0.3427 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7040  Z= 0.355
  Angle     :  0.684   7.754   9470  Z= 0.355
  Chirality :  0.051   0.138   1180
  Planarity :  0.002   0.013   1180
  Dihedral  :  8.481  46.274   1100
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers : 12.35 %
    Allowed  : 17.35 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  50 
 PHE   0.017   0.003   PHE C  94 

*********************** 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
  258 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 174
  time to evaluate  : 0.789 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8718 (mtpp)
REVERT: C   13 GLU cc_start: 0.8295 (tp30) cc_final: 0.8076 (tp30)
REVERT: C   28 GLU cc_start: 0.8177 (tt0) cc_final: 0.7951 (mt-10)
REVERT: D    2 ASP cc_start: 0.8821 (p0) cc_final: 0.8387 (p0)
REVERT: D    8 LEU cc_start: 0.9198 (mm) cc_final: 0.8839 (mm)
REVERT: E   32 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8586 (mtpt)
REVERT: F   13 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: F   28 GLU cc_start: 0.8262 (tt0) cc_final: 0.8038 (mt-10)
REVERT: G   13 GLU cc_start: 0.8032 (tp30) cc_final: 0.7575 (tp30)
REVERT: G   32 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8656 (mtpt)
REVERT: J    2 ASP cc_start: 0.8839 (p0) cc_final: 0.8624 (p0)
  outliers start: 84
  outliers final: 76
  residues processed: 230
  average time/residue: 0.1247
  time to fit residues: 42.6258
Evaluate side-chains
  249 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 173
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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   74 VAL
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   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   55 VAL
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   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   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   70 VAL
Chi-restraints excluded: chain F residue   74 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   54 THR
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    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   72 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.111442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.097411 restraints weight = 11018.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.81
r_work: 0.3389 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048   7040  Z= 0.526
  Angle     :  0.779   8.462   9470  Z= 0.408
  Chirality :  0.055   0.178   1180
  Planarity :  0.003   0.015   1180
  Dihedral  :  8.814  44.861   1100
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers : 12.94 %
    Allowed  : 17.21 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.31 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.14), residues: 950

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

*********************** 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
  254 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 166
  time to evaluate  : 0.824 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8881 (mtpp)
REVERT: C   28 GLU cc_start: 0.8310 (tt0) cc_final: 0.8040 (mt-10)
REVERT: D    2 ASP cc_start: 0.8811 (p0) cc_final: 0.8388 (p0)
REVERT: E   32 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8756 (mtpt)
REVERT: F   13 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: G   32 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8724 (mtpt)
  outliers start: 88
  outliers final: 84
  residues processed: 230
  average time/residue: 0.1228
  time to fit residues: 42.1000
Evaluate side-chains
  247 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 163
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
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   74 VAL
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   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   44 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   55 VAL
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    8 LEU
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   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   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   70 VAL
Chi-restraints excluded: chain F residue   74 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   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    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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0970
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   overall best weight:    3.2184

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.113104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.099007 restraints weight = 10863.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.81
r_work: 0.3416 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   7040  Z= 0.409
  Angle     :  0.724   8.269   9470  Z= 0.376
  Chirality :  0.053   0.134   1180
  Planarity :  0.002   0.014   1180
  Dihedral  :  8.600  46.116   1100
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers : 12.79 %
    Allowed  : 17.21 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.14), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS G  50 
 PHE   0.018   0.003   PHE C  94 

*********************** 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
  257 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 170
  time to evaluate  : 0.833 
Fit side-chains
REVERT: B   13 GLU cc_start: 0.8094 (tp30) cc_final: 0.7817 (tp30)
REVERT: B   32 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8719 (mtpp)
REVERT: B   83 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7272 (mp0)
REVERT: C   28 GLU cc_start: 0.8172 (tt0) cc_final: 0.7935 (mt-10)
REVERT: D    2 ASP cc_start: 0.8822 (p0) cc_final: 0.8420 (p0)
REVERT: D    8 LEU cc_start: 0.9206 (mm) cc_final: 0.8847 (mm)
REVERT: E   32 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8620 (mtpt)
REVERT: G   32 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8623 (mtpt)
REVERT: J   28 GLU cc_start: 0.8119 (tt0) cc_final: 0.7914 (mt-10)
  outliers start: 87
  outliers final: 83
  residues processed: 230
  average time/residue: 0.1242
  time to fit residues: 42.5987
Evaluate side-chains
  251 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 167
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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   74 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   83 GLU
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   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   54 THR
Chi-restraints excluded: chain D residue   55 VAL
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   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   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   70 VAL
Chi-restraints excluded: chain F residue   74 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   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    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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.3723 r_free = 0.3723 target = 0.112661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.098515 restraints weight = 10974.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.81
r_work: 0.3408 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   7040  Z= 0.430
  Angle     :  0.743   8.376   9470  Z= 0.386
  Chirality :  0.053   0.135   1180
  Planarity :  0.002   0.013   1180
  Dihedral  :  8.587  45.797   1100
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers : 13.24 %
    Allowed  : 16.76 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.19), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B  50 
 PHE   0.019   0.003   PHE C  94 

*********************** 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
  256 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 166
  time to evaluate  : 0.823 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8718 (mtpp)
REVERT: B   83 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7279 (mp0)
REVERT: C   28 GLU cc_start: 0.8179 (tt0) cc_final: 0.7930 (mt-10)
REVERT: C   62 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8103 (tt0)
REVERT: D    2 ASP cc_start: 0.8709 (p0) cc_final: 0.8303 (p0)
REVERT: D    8 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8824 (mm)
REVERT: E   32 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8656 (mtpt)
REVERT: G   32 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8648 (mtpt)
REVERT: J   28 GLU cc_start: 0.8237 (tt0) cc_final: 0.7993 (mt-10)
  outliers start: 90
  outliers final: 83
  residues processed: 229
  average time/residue: 0.1235
  time to fit residues: 41.8636
Evaluate side-chains
  251 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 165
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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   74 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   83 GLU
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   62 GLN
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    8 LEU
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   55 VAL
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   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   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   70 VAL
Chi-restraints excluded: chain F residue   74 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   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    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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.114581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.100424 restraints weight = 10978.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.84
r_work: 0.3440 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7040  Z= 0.330
  Angle     :  0.696   8.654   9470  Z= 0.360
  Chirality :  0.051   0.134   1180
  Planarity :  0.002   0.016   1180
  Dihedral  :  8.387  47.818   1100
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers : 12.65 %
    Allowed  : 17.50 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.10 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS C  50 
 PHE   0.016   0.003   PHE C  94 

*********************** 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
  259 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 173
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: B   32 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8695 (mtpp)
REVERT: B   83 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7233 (mp0)
REVERT: D    2 ASP cc_start: 0.8640 (p0) cc_final: 0.8240 (p0)
REVERT: D    8 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8846 (mm)
REVERT: E   32 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8595 (mtpt)
REVERT: J   28 GLU cc_start: 0.8226 (tt0) cc_final: 0.7990 (mt-10)
  outliers start: 86
  outliers final: 81
  residues processed: 230
  average time/residue: 0.1293
  time to fit residues: 44.2564
Evaluate side-chains
  255 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 172
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
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 B residue   83 GLU
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   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    8 LEU
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   55 VAL
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   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   74 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    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   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   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    8 LEU
Chi-restraints excluded: chain I residue   22 THR
Chi-restraints excluded: chain I residue   54 THR
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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 96 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.115891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.101599 restraints weight = 10912.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.84
r_work: 0.3457 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7040  Z= 0.286
  Angle     :  0.683   8.816   9470  Z= 0.352
  Chirality :  0.050   0.136   1180
  Planarity :  0.002   0.018   1180
  Dihedral  :  8.240  48.806   1100
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers : 12.35 %
    Allowed  : 18.09 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.15), residues: 950

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

********************** 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
  258 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 174
  time to evaluate  : 0.832 
Fit side-chains
REVERT: B   32 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8709 (mtpp)
REVERT: B   83 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7210 (mp0)
REVERT: C   13 GLU cc_start: 0.8355 (tp30) cc_final: 0.8124 (tp30)
REVERT: D    2 ASP cc_start: 0.8620 (p0) cc_final: 0.8196 (p0)
REVERT: D    8 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8842 (mm)
REVERT: E   32 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8643 (mtpt)
REVERT: G   32 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8715 (mtpp)
  outliers start: 84
  outliers final: 81
  residues processed: 229
  average time/residue: 0.1217
  time to fit residues: 41.5399
Evaluate side-chains
  254 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 171
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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   22 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 B residue   83 GLU
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   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    8 LEU
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   55 VAL
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   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   74 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    8 LEU
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   54 THR
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   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    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   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
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 4 optimal weight:    0.4980
   chunk 19 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    2.4762

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.114944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.100673 restraints weight = 10881.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.83
r_work: 0.3447 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7040  Z= 0.326
  Angle     :  0.694   8.895   9470  Z= 0.358
  Chirality :  0.051   0.132   1180
  Planarity :  0.002   0.016   1180
  Dihedral  :  8.290  47.770   1100
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers : 12.94 %
    Allowed  : 17.79 %
    Favored  : 69.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.20), residues: 950
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.15), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS G  50 
 PHE   0.016   0.003   PHE C  94 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2948.80 seconds
wall clock time: 53 minutes 35.13 seconds (3215.13 seconds total)