Starting phenix.real_space_refine
on Tue Jun 10 08:19:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sc0_25007/06_2025/7sc0_25007.cif"
  }
  resolution = 3.4
  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=   0.039
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    7766      2.51       5
     N    1826      2.21       5
     O    2002      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11638
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1058
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J
  Time building chain proxies: 4.18, per 1000 atoms: 0.36
  Number of scatterers: 11638
  At special positions: 0
  Unit cell: (147.98, 148.96, 50.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    2002      8.00
     N    1826      7.00
     C    7766      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: 2.86
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2728

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 1 sheets defined
      72.1% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 71
    Processing helix  chain 'A' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA A  87 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 100 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG A 101 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 129
      removed outlier: 3.703A  pdb=" N   ALA A 112 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 113 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP A 115 " --> pdb=" O   MET A 111 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A 140 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA A 162 " --> pdb=" O   PRO A 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 158 through 163'
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 4.036A  pdb=" N   PHE A 167 " --> pdb=" O   GLY A 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 71
    Processing helix  chain 'B' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR B 100 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG B 101 " --> pdb=" O   TYR B  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA B 112 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU B 113 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ILE B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP B 115 " --> pdb=" O   MET B 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 121 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 122 " --> pdb=" O   TYR B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU B 138 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE B 139 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU B 140 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 156
    Processing helix  chain 'B' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA B 162 " --> pdb=" O   PRO B 158 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 158 through 163'
    Processing helix  chain 'B' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE B 167 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA C  87 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE C  89 " --> pdb=" O   TRP C  85 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS C  96 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR C 100 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG C 101 " --> pdb=" O   TYR C  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE C 107 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA C 112 " --> pdb=" O   GLY C 108 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU C 113 " --> pdb=" O   ILE C 109 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ILE C 114 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP C 115 " --> pdb=" O   MET C 111 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE C 121 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU C 122 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU C 138 " --> pdb=" O   ILE C 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE C 139 " --> pdb=" O   LYS C 135 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 156
    Processing helix  chain 'C' and resid 158 through 163
      removed outlier: 3.564A  pdb=" N   ALA C 162 " --> pdb=" O   PRO C 158 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL C 163 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 158 through 163'
    Processing helix  chain 'C' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE C 167 " --> pdb=" O   GLY C 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE D  89 " --> pdb=" O   TRP D  85 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR D  90 " --> pdb=" O   LYS D  86 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS D  96 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR D 100 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG D 101 " --> pdb=" O   TYR D  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA D 112 " --> pdb=" O   GLY D 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU D 113 " --> pdb=" O   ILE D 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE D 114 " --> pdb=" O   PRO D 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP D 115 " --> pdb=" O   MET D 111 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA D 120 " --> pdb=" O   GLY D 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE D 121 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU D 122 " --> pdb=" O   TYR D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU D 138 " --> pdb=" O   ILE D 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE D 139 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU D 140 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 156
    Processing helix  chain 'D' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA D 162 " --> pdb=" O   PRO D 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL D 163 " --> pdb=" O   LEU D 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 158 through 163'
    Processing helix  chain 'D' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE D 167 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 71
    Processing helix  chain 'E' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA E  87 " --> pdb=" O   GLY E  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE E  89 " --> pdb=" O   TRP E  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR E  90 " --> pdb=" O   LYS E  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS E  96 " --> pdb=" O   PHE E  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR E 100 " --> pdb=" O   LYS E  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG E 101 " --> pdb=" O   TYR E  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE E 107 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 129
      removed outlier: 3.705A  pdb=" N   ALA E 112 " --> pdb=" O   GLY E 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU E 113 " --> pdb=" O   ILE E 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE E 114 " --> pdb=" O   PRO E 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP E 115 " --> pdb=" O   MET E 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA E 120 " --> pdb=" O   GLY E 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE E 121 " --> pdb=" O   ILE E 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU E 122 " --> pdb=" O   TYR E 118 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU E 138 " --> pdb=" O   ILE E 134 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE E 139 " --> pdb=" O   LYS E 135 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU E 140 " --> pdb=" O   SER E 136 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 142 through 156
    Processing helix  chain 'E' and resid 158 through 163
      removed outlier: 3.564A  pdb=" N   ALA E 162 " --> pdb=" O   PRO E 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL E 163 " --> pdb=" O   LEU E 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 158 through 163'
    Processing helix  chain 'E' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE E 167 " --> pdb=" O   GLY E 164 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 71
    Processing helix  chain 'F' and resid 81 through 107
      removed outlier: 4.367A  pdb=" N   ALA F  87 " --> pdb=" O   GLY F  83 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE F  89 " --> pdb=" O   TRP F  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR F  90 " --> pdb=" O   LYS F  86 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS F  96 " --> pdb=" O   PHE F  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR F 100 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG F 101 " --> pdb=" O   TYR F  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE F 107 " --> pdb=" O   LEU F 103 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA F 112 " --> pdb=" O   GLY F 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU F 113 " --> pdb=" O   ILE F 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE F 114 " --> pdb=" O   PRO F 110 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP F 115 " --> pdb=" O   MET F 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA F 120 " --> pdb=" O   GLY F 116 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE F 121 " --> pdb=" O   ILE F 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU F 122 " --> pdb=" O   TYR F 118 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU F 138 " --> pdb=" O   ILE F 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE F 139 " --> pdb=" O   LYS F 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU F 140 " --> pdb=" O   SER F 136 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 142 through 156
    Processing helix  chain 'F' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA F 162 " --> pdb=" O   PRO F 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL F 163 " --> pdb=" O   LEU F 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 158 through 163'
    Processing helix  chain 'F' and resid 164 through 168
      removed outlier: 4.036A  pdb=" N   PHE F 167 " --> pdb=" O   GLY F 164 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 67 through 71
    Processing helix  chain 'G' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA G  87 " --> pdb=" O   GLY G  83 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE G  89 " --> pdb=" O   TRP G  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR G  90 " --> pdb=" O   LYS G  86 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS G  96 " --> pdb=" O   PHE G  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR G 100 " --> pdb=" O   LYS G  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG G 101 " --> pdb=" O   TYR G  97 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE G 107 " --> pdb=" O   LEU G 103 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 108 through 129
      removed outlier: 3.705A  pdb=" N   ALA G 112 " --> pdb=" O   GLY G 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU G 113 " --> pdb=" O   ILE G 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE G 114 " --> pdb=" O   PRO G 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP G 115 " --> pdb=" O   MET G 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA G 120 " --> pdb=" O   GLY G 116 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE G 121 " --> pdb=" O   ILE G 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU G 122 " --> pdb=" O   TYR G 118 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU G 138 " --> pdb=" O   ILE G 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE G 139 " --> pdb=" O   LYS G 135 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU G 140 " --> pdb=" O   SER G 136 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 142 through 156
    Processing helix  chain 'G' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA G 162 " --> pdb=" O   PRO G 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL G 163 " --> pdb=" O   LEU G 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 158 through 163'
    Processing helix  chain 'G' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE G 167 " --> pdb=" O   GLY G 164 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 67 through 71
    Processing helix  chain 'H' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA H  87 " --> pdb=" O   GLY H  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE H  89 " --> pdb=" O   TRP H  85 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   THR H  90 " --> pdb=" O   LYS H  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS H  96 " --> pdb=" O   PHE H  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR H 100 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG H 101 " --> pdb=" O   TYR H  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE H 107 " --> pdb=" O   LEU H 103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA H 112 " --> pdb=" O   GLY H 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU H 113 " --> pdb=" O   ILE H 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE H 114 " --> pdb=" O   PRO H 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP H 115 " --> pdb=" O   MET H 111 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA H 120 " --> pdb=" O   GLY H 116 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE H 121 " --> pdb=" O   ILE H 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU H 122 " --> pdb=" O   TYR H 118 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU H 138 " --> pdb=" O   ILE H 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE H 139 " --> pdb=" O   LYS H 135 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU H 140 " --> pdb=" O   SER H 136 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 142 through 156
    Processing helix  chain 'H' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA H 162 " --> pdb=" O   PRO H 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL H 163 " --> pdb=" O   LEU H 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 158 through 163'
    Processing helix  chain 'H' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE H 167 " --> pdb=" O   GLY H 164 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 67 through 71
    Processing helix  chain 'I' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA I  87 " --> pdb=" O   GLY I  83 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE I  89 " --> pdb=" O   TRP I  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR I  90 " --> pdb=" O   LYS I  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS I  96 " --> pdb=" O   PHE I  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR I 100 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG I 101 " --> pdb=" O   TYR I  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE I 107 " --> pdb=" O   LEU I 103 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 108 through 129
      removed outlier: 3.705A  pdb=" N   ALA I 112 " --> pdb=" O   GLY I 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU I 113 " --> pdb=" O   ILE I 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE I 114 " --> pdb=" O   PRO I 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP I 115 " --> pdb=" O   MET I 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA I 120 " --> pdb=" O   GLY I 116 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU I 122 " --> pdb=" O   TYR I 118 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 129 through 141
      removed outlier: 3.845A  pdb=" N   LEU I 138 " --> pdb=" O   ILE I 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE I 139 " --> pdb=" O   LYS I 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU I 140 " --> pdb=" O   SER I 136 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 142 through 156
    Processing helix  chain 'I' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA I 162 " --> pdb=" O   PRO I 158 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL I 163 " --> pdb=" O   LEU I 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 158 through 163'
    Processing helix  chain 'I' and resid 164 through 168
      removed outlier: 4.038A  pdb=" N   PHE I 167 " --> pdb=" O   GLY I 164 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 67 through 71
    Processing helix  chain 'J' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA J  87 " --> pdb=" O   GLY J  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE J  89 " --> pdb=" O   TRP J  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR J  90 " --> pdb=" O   LYS J  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS J  96 " --> pdb=" O   PHE J  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR J 100 " --> pdb=" O   LYS J  96 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG J 101 " --> pdb=" O   TYR J  97 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE J 107 " --> pdb=" O   LEU J 103 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA J 112 " --> pdb=" O   GLY J 108 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU J 113 " --> pdb=" O   ILE J 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE J 114 " --> pdb=" O   PRO J 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TRP J 115 " --> pdb=" O   MET J 111 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA J 120 " --> pdb=" O   GLY J 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE J 121 " --> pdb=" O   ILE J 117 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU J 122 " --> pdb=" O   TYR J 118 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU J 138 " --> pdb=" O   ILE J 134 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE J 139 " --> pdb=" O   LYS J 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU J 140 " --> pdb=" O   SER J 136 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 142 through 156
    Processing helix  chain 'J' and resid 158 through 163
      removed outlier: 3.564A  pdb=" N   ALA J 162 " --> pdb=" O   PRO J 158 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL J 163 " --> pdb=" O   LEU J 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 158 through 163'
    Processing helix  chain 'J' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE J 167 " --> pdb=" O   GLY J 164 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 67 through 71
    Processing helix  chain 'K' and resid 81 through 107
      removed outlier: 4.368A  pdb=" N   ALA K  87 " --> pdb=" O   GLY K  83 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE K  89 " --> pdb=" O   TRP K  85 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR K  90 " --> pdb=" O   LYS K  86 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS K  96 " --> pdb=" O   PHE K  92 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR K 100 " --> pdb=" O   LYS K  96 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG K 101 " --> pdb=" O   TYR K  97 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE K 107 " --> pdb=" O   LEU K 103 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 108 through 129
      removed outlier: 3.704A  pdb=" N   ALA K 112 " --> pdb=" O   GLY K 108 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU K 113 " --> pdb=" O   ILE K 109 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE K 114 " --> pdb=" O   PRO K 110 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP K 115 " --> pdb=" O   MET K 111 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA K 120 " --> pdb=" O   GLY K 116 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE K 121 " --> pdb=" O   ILE K 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU K 122 " --> pdb=" O   TYR K 118 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 129 through 141
      removed outlier: 3.846A  pdb=" N   LEU K 138 " --> pdb=" O   ILE K 134 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE K 139 " --> pdb=" O   LYS K 135 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU K 140 " --> pdb=" O   SER K 136 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 142 through 156
    Processing helix  chain 'K' and resid 158 through 163
      removed outlier: 3.565A  pdb=" N   ALA K 162 " --> pdb=" O   PRO K 158 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL K 163 " --> pdb=" O   LEU K 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 158 through 163'
    Processing helix  chain 'K' and resid 164 through 168
      removed outlier: 4.037A  pdb=" N   PHE K 167 " --> pdb=" O   GLY K 164 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 176
      removed outlier: 3.690A  pdb=" N   VAL A 170 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN B 175 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 174 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL B 170 " --> pdb=" O   ARG C 171 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN C 175 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU B 174 " --> pdb=" O   GLN C 175 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C 170 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLN D 175 " --> pdb=" O   ILE C 172 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU C 174 " --> pdb=" O   GLN D 175 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL D 170 " --> pdb=" O   ARG E 171 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN E 175 " --> pdb=" O   ILE D 172 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 174 " --> pdb=" O   GLN E 175 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL E 170 " --> pdb=" O   ARG F 171 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN F 175 " --> pdb=" O   ILE E 172 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU E 174 " --> pdb=" O   GLN F 175 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL F 170 " --> pdb=" O   ARG G 171 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLN G 175 " --> pdb=" O   ILE F 172 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU F 174 " --> pdb=" O   GLN G 175 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL G 170 " --> pdb=" O   ARG H 171 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN H 175 " --> pdb=" O   ILE G 172 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU G 174 " --> pdb=" O   GLN H 175 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL H 170 " --> pdb=" O   ARG I 171 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN I 175 " --> pdb=" O   ILE H 172 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU H 174 " --> pdb=" O   GLN I 175 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL I 170 " --> pdb=" O   ARG J 171 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN J 175 " --> pdb=" O   ILE I 172 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU I 174 " --> pdb=" O   GLN J 175 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL J 170 " --> pdb=" O   ARG K 171 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN K 175 " --> pdb=" O   ILE J 172 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU J 174 " --> pdb=" O   GLN K 175 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG A 171 " --> pdb=" O   VAL K 170 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   ILE K 172 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ASN A 173 " --> pdb=" O   ILE K 172 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   LEU K 174 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN A 175 " --> pdb=" O   LEU K 174 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   LYS K 176 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)

    538 hydrogen bonds defined for protein.
    1515 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: 2.61

  Time building geometry restraints manager: 3.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3476
        1.34 -     1.46: 3024
        1.46 -     1.58: 5435
        1.58 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 11990
  Sorted by residual:
  bond pdb=" C   ILE G 109 "
       pdb=" N   PRO G 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.08e-02 8.57e+03 2.79e+00
  bond pdb=" C   ILE J 109 "
       pdb=" N   PRO J 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.08e-02 8.57e+03 2.79e+00
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.08e-02 8.57e+03 2.79e+00
  bond pdb=" C   ILE F 109 "
       pdb=" N   PRO F 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.08e-02 8.57e+03 2.73e+00
  bond pdb=" C   ILE H 109 "
       pdb=" N   PRO H 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.08e-02 8.57e+03 2.73e+00
  ... (remaining 11985 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 15533
        0.98 -     1.97: 608
        1.97 -     2.95: 108
        2.95 -     3.94: 42
        3.94 -     4.92: 44
  Bond angle restraints: 16335
  Sorted by residual:
  angle pdb=" C   ASN D  53 "
        pdb=" N   ARG D  54 "
        pdb=" CA  ARG D  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.99e+00
  angle pdb=" C   ASN K  53 "
        pdb=" N   ARG K  54 "
        pdb=" CA  ARG K  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.98e+00
  angle pdb=" C   ASN A  53 "
        pdb=" N   ARG A  54 "
        pdb=" CA  ARG A  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.97e+00
  angle pdb=" C   ASN J  53 "
        pdb=" N   ARG J  54 "
        pdb=" CA  ARG J  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.20   -4.66 1.91e+00 2.74e-01 5.94e+00
  angle pdb=" C   ASN G  53 "
        pdb=" N   ARG G  54 "
        pdb=" CA  ARG G  54 "
      ideal   model   delta    sigma   weight residual
     121.54  126.19   -4.65 1.91e+00 2.74e-01 5.93e+00
  ... (remaining 16330 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 6578
       17.70 -    35.39: 275
       35.39 -    53.09: 22
       53.09 -    70.79: 0
       70.79 -    88.48: 11
  Dihedral angle restraints: 6886
    sinusoidal: 2695
      harmonic: 4191
  Sorted by residual:
  dihedral pdb=" CB  GLU G  76 "
           pdb=" CG  GLU G  76 "
           pdb=" CD  GLU G  76 "
           pdb=" OE1 GLU G  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.48  -88.48     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU K  76 "
           pdb=" CG  GLU K  76 "
           pdb=" CD  GLU K  76 "
           pdb=" OE1 GLU K  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.48  -88.48     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU C  76 "
           pdb=" CG  GLU C  76 "
           pdb=" CD  GLU C  76 "
           pdb=" OE1 GLU C  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.48  -88.48     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 6883 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1444
       0.046 -    0.093: 319
       0.093 -    0.139: 85
       0.139 -    0.185: 0
       0.185 -    0.231: 11
  Chirality restraints: 1859
  Sorted by residual:
  chirality pdb=" CB  ILE G 141 "
            pdb=" CA  ILE G 141 "
            pdb=" CG1 ILE G 141 "
            pdb=" CG2 ILE G 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CB  ILE I 141 "
            pdb=" CA  ILE I 141 "
            pdb=" CG1 ILE I 141 "
            pdb=" CG2 ILE I 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B 141 "
            pdb=" CA  ILE B 141 "
            pdb=" CG1 ILE B 141 "
            pdb=" CG2 ILE B 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1856 not shown)

  Planarity restraints: 1991
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 109 "   -0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO F 110 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO F 110 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F 110 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 109 "    0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO A 110 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE K 109 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO K 110 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO K 110 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO K 110 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1988 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 5110
        2.96 -     3.45: 10121
        3.45 -     3.93: 16712
        3.93 -     4.42: 17201
        4.42 -     4.90: 31692
  Nonbonded interactions: 80836
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 165 "
            pdb=" OD1 ASP K 157 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" OD1 ASP B 157 "
            pdb=" NZ  LYS C 165 "
     model   vdw
     2.483 3.120
  nonbonded pdb=" OD1 ASP A 157 "
            pdb=" NZ  LYS B 165 "
     model   vdw
     2.485 3.120
  nonbonded pdb=" OD1 ASP E 157 "
            pdb=" NZ  LYS F 165 "
     model   vdw
     2.485 3.120
  nonbonded pdb=" OD1 ASP I 157 "
            pdb=" NZ  LYS J 165 "
     model   vdw
     2.488 3.120
  ... (remaining 80831 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
}

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:             4.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     24.070
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11990  Z= 0.125
  Angle     :  0.523   4.922  16335  Z= 0.305
  Chirality :  0.043   0.231   1859
  Planarity :  0.003   0.031   1991
  Dihedral  : 10.005  88.483   4158
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.84 (0.20), residues: 1397
  helix: -0.90 (0.16), residues: 814
  sheet:  None (None), residues: 0
  loop : -3.37 (0.23), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 128 
 HIS   0.001   0.000   HIS I 153 
 PHE   0.006   0.001   PHE H 137 
 TYR   0.004   0.001   TYR I 148 
 ARG   0.001   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.42725 (  538)
  hydrogen bonds       : angle       6.13304 ( 1515)
  covalent geometry    : bond        0.00251 (11990)
  covalent geometry    : angle       0.52338 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.278 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2737
  time to fit residues: 55.3600
Evaluate side-chains
  129 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3873 r_free = 0.3873 target = 0.156975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134149 restraints weight = 14253.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.88
r_work: 0.3477 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11990  Z= 0.195
  Angle     :  0.618   5.897  16335  Z= 0.355
  Chirality :  0.047   0.145   1859
  Planarity :  0.004   0.031   1991
  Dihedral  :  4.416  16.337   1507
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  8.30 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.89 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.22), residues: 1397
  helix:  0.07 (0.18), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.17 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP I 128 
 HIS   0.004   0.001   HIS I 126 
 PHE   0.019   0.002   PHE H 107 
 TYR   0.008   0.001   TYR C 148 
 ARG   0.001   0.000   ARG E 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10891 (  538)
  hydrogen bonds       : angle       4.03391 ( 1515)
  covalent geometry    : bond        0.00393 (11990)
  covalent geometry    : angle       0.61796 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 158
  time to evaluate  : 1.296 
Fit side-chains
REVERT: I   61 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7606 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 162
  average time/residue: 0.2392
  time to fit residues: 54.9384
Evaluate side-chains
  152 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain I residue   61 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 11 optimal weight:    0.0010
   chunk 77 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0050
   chunk 117 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   overall best weight:    0.5000

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.164172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.141821 restraints weight = 14417.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.88
r_work: 0.3544 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11990  Z= 0.147
  Angle     :  0.517   4.618  16335  Z= 0.295
  Chirality :  0.043   0.125   1859
  Planarity :  0.003   0.030   1991
  Dihedral  :  4.349  16.140   1507
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  4.74 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.23), residues: 1397
  helix:  0.51 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.19 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  98 
 HIS   0.002   0.001   HIS H 126 
 PHE   0.011   0.001   PHE C 137 
 TYR   0.007   0.001   TYR J 148 
 ARG   0.001   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08725 (  538)
  hydrogen bonds       : angle       3.76953 ( 1515)
  covalent geometry    : bond        0.00282 (11990)
  covalent geometry    : angle       0.51732 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 1.390 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7735 (m-30)
REVERT: I   61 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7525 (m-30)
  outliers start: 35
  outliers final: 26
  residues processed: 189
  average time/residue: 0.2727
  time to fit residues: 71.6119
Evaluate side-chains
  181 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  175 GLN
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  175 GLN
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain E residue  175 GLN
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain F residue  175 GLN
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain G residue  175 GLN
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  175 GLN
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   69 GLU
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0010
   chunk 34 optimal weight:    2.9990
   chunk 131 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.4586

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.164848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.142656 restraints weight = 14256.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.85
r_work: 0.3539 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11990  Z= 0.137
  Angle     :  0.500   4.648  16335  Z= 0.284
  Chirality :  0.042   0.124   1859
  Planarity :  0.004   0.032   1991
  Dihedral  :  4.220  15.623   1507
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 0.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  6.06 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.23), residues: 1397
  helix:  0.60 (0.19), residues: 847
  sheet:  None (None), residues: 0
  loop : -3.01 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  98 
 HIS   0.002   0.000   HIS J 126 
 PHE   0.011   0.001   PHE C 137 
 TYR   0.006   0.001   TYR H 148 
 ARG   0.001   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07580 (  538)
  hydrogen bonds       : angle       3.65815 ( 1515)
  covalent geometry    : bond        0.00273 (11990)
  covalent geometry    : angle       0.50036 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 1.235 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7745 (m-30)
REVERT: I   61 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7645 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 162
  average time/residue: 0.2518
  time to fit residues: 56.7475
Evaluate side-chains
  160 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain I residue   59 LEU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  175 GLN
Chi-restraints excluded: chain K residue  154 THR
Chi-restraints excluded: chain K residue  175 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0670
   chunk 1 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 125 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.160785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140453 restraints weight = 14044.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.63
r_work: 0.3571 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11990  Z= 0.149
  Angle     :  0.516   4.600  16335  Z= 0.293
  Chirality :  0.043   0.131   1859
  Planarity :  0.003   0.030   1991
  Dihedral  :  4.203  15.421   1507
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  9.59 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  :  5.59 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.23), residues: 1397
  helix:  0.76 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.10 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP I 115 
 HIS   0.002   0.001   HIS J 126 
 PHE   0.014   0.002   PHE C 137 
 TYR   0.006   0.001   TYR J 148 
 ARG   0.001   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08305 (  538)
  hydrogen bonds       : angle       3.70261 ( 1515)
  covalent geometry    : bond        0.00312 (11990)
  covalent geometry    : angle       0.51616 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 1.354 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7886 (t0)
REVERT: I   61 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7641 (m-30)
  outliers start: 42
  outliers final: 30
  residues processed: 160
  average time/residue: 0.2630
  time to fit residues: 59.2885
Evaluate side-chains
  177 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 1.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain G residue  175 GLN
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   59 LEU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain J residue  175 GLN
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 110 optimal weight:    0.2980
   chunk 81 optimal weight:    0.2980
   chunk 116 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.167531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.146230 restraints weight = 14353.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 1.76
r_work: 0.3593 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11990  Z= 0.127
  Angle     :  0.482   4.527  16335  Z= 0.272
  Chirality :  0.041   0.122   1859
  Planarity :  0.003   0.031   1991
  Dihedral  :  4.209  15.866   1507
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  6.37 %
    Favored  : 90.68 %
  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: -0.99 (0.24), residues: 1397
  helix:  0.86 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.18 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  98 
 HIS   0.002   0.000   HIS H 126 
 PHE   0.008   0.001   PHE C  89 
 TYR   0.008   0.001   TYR E  97 
 ARG   0.001   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06965 (  538)
  hydrogen bonds       : angle       3.59801 ( 1515)
  covalent geometry    : bond        0.00252 (11990)
  covalent geometry    : angle       0.48245 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 1.558 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7768 (t0)
REVERT: C   49 ILE cc_start: 0.7351 (mm) cc_final: 0.6660 (mm)
REVERT: I   61 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7577 (m-30)
  outliers start: 38
  outliers final: 24
  residues processed: 164
  average time/residue: 0.2750
  time to fit residues: 62.7520
Evaluate side-chains
  176 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue   69 GLU
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain F residue  175 GLN
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   59 LEU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0970
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 128 optimal weight:    0.4980
   chunk 108 optimal weight:    0.1980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.162220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.141698 restraints weight = 14205.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.65
r_work: 0.3595 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11990  Z= 0.133
  Angle     :  0.492   4.527  16335  Z= 0.277
  Chirality :  0.042   0.127   1859
  Planarity :  0.003   0.030   1991
  Dihedral  :  4.168  15.343   1507
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  :  6.76 %
    Favored  : 90.44 %
  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: -0.95 (0.24), residues: 1397
  helix:  0.90 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.19 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP D  98 
 HIS   0.002   0.000   HIS H 126 
 PHE   0.012   0.001   PHE J  81 
 TYR   0.006   0.001   TYR J 148 
 ARG   0.004   0.000   ARG K 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07357 (  538)
  hydrogen bonds       : angle       3.61096 ( 1515)
  covalent geometry    : bond        0.00271 (11990)
  covalent geometry    : angle       0.49226 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 1.409 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (t0)
REVERT: E   61 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7825 (m-30)
REVERT: I   61 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7640 (m-30)
  outliers start: 36
  outliers final: 25
  residues processed: 155
  average time/residue: 0.2677
  time to fit residues: 57.5996
Evaluate side-chains
  174 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   59 LEU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   59 LEU
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue   69 GLU
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.161585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140289 restraints weight = 14810.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.74
r_work: 0.3476 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11990  Z= 0.195
  Angle     :  0.575   4.699  16335  Z= 0.331
  Chirality :  0.045   0.146   1859
  Planarity :  0.004   0.029   1991
  Dihedral  :  4.262  14.761   1507
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 10.31 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  7.07 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.23), residues: 1397
  helix:  0.75 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.24 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I 128 
 HIS   0.003   0.001   HIS C 126 
 PHE   0.019   0.002   PHE J  81 
 TYR   0.009   0.001   TYR E  97 
 ARG   0.002   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09836 (  538)
  hydrogen bonds       : angle       3.81504 ( 1515)
  covalent geometry    : bond        0.00449 (11990)
  covalent geometry    : angle       0.57502 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 166
  time to evaluate  : 1.185 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7901 (m-30)
REVERT: G   49 ILE cc_start: 0.7402 (mm) cc_final: 0.6763 (mm)
REVERT: I   61 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7790 (m-30)
  outliers start: 35
  outliers final: 23
  residues processed: 177
  average time/residue: 0.2455
  time to fit residues: 61.3405
Evaluate side-chains
  185 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain H residue   69 GLU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0270
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 109 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 119 optimal weight:    0.1980
   overall best weight:    0.4038

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.164815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.143772 restraints weight = 14441.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.72
r_work: 0.3565 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11990  Z= 0.131
  Angle     :  0.498   5.458  16335  Z= 0.281
  Chirality :  0.042   0.123   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.353  17.562   1507
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  :  7.93 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.24), residues: 1397
  helix:  0.87 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.24 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  98 
 HIS   0.002   0.000   HIS J 126 
 PHE   0.012   0.001   PHE J  81 
 TYR   0.016   0.001   TYR J  97 
 ARG   0.001   0.000   ARG K 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07233 (  538)
  hydrogen bonds       : angle       3.63788 ( 1515)
  covalent geometry    : bond        0.00254 (11990)
  covalent geometry    : angle       0.49777 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 1.318 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7832 (m-30)
REVERT: G   49 ILE cc_start: 0.7422 (mm) cc_final: 0.6762 (mm)
REVERT: I   61 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7669 (m-30)
  outliers start: 34
  outliers final: 24
  residues processed: 169
  average time/residue: 0.2564
  time to fit residues: 60.5306
Evaluate side-chains
  189 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   59 LEU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   61 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.163504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.142357 restraints weight = 14581.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.72
r_work: 0.3522 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11990  Z= 0.164
  Angle     :  0.538   4.621  16335  Z= 0.307
  Chirality :  0.043   0.137   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.270  16.041   1507
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 0.60
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  9.74 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.70 %
    Favored  : 89.43 %
  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: -0.98 (0.24), residues: 1397
  helix:  0.88 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.21 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  98 
 HIS   0.002   0.001   HIS C 126 
 PHE   0.017   0.002   PHE J  81 
 TYR   0.016   0.001   TYR F  97 
 ARG   0.002   0.000   ARG K 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08813 (  538)
  hydrogen bonds       : angle       3.72947 ( 1515)
  covalent geometry    : bond        0.00357 (11990)
  covalent geometry    : angle       0.53786 (16335)

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

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

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2794 Ramachandran restraints generated.
    1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 1.226 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7938 (m-30)
REVERT: G   49 ILE cc_start: 0.7584 (mm) cc_final: 0.6913 (mm)
REVERT: I   49 ILE cc_start: 0.7620 (mm) cc_final: 0.7200 (mm)
REVERT: I   61 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7693 (m-30)
  outliers start: 24
  outliers final: 22
  residues processed: 176
  average time/residue: 0.2383
  time to fit residues: 59.0033
Evaluate side-chains
  187 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   61 ASP
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain E residue   61 ASP
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain I residue  154 THR
Chi-restraints excluded: chain J residue  154 THR
Chi-restraints excluded: chain K residue   61 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 116 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0010
   chunk 128 optimal weight:    0.3980
   chunk 118 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0010
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.3192

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.166923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145897 restraints weight = 14184.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.71
r_work: 0.3571 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11990  Z= 0.124
  Angle     :  0.488   4.525  16335  Z= 0.273
  Chirality :  0.042   0.129   1859
  Planarity :  0.003   0.030   1991
  Dihedral  :  4.292  16.038   1507
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  8.55 %
    Favored  : 89.36 %
  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: -0.90 (0.24), residues: 1397
  helix:  0.96 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.21 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  98 
 HIS   0.002   0.000   HIS G 126 
 PHE   0.012   0.001   PHE J  81 
 TYR   0.016   0.001   TYR F  97 
 ARG   0.004   0.000   ARG K 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06685 (  538)
  hydrogen bonds       : angle       3.59406 ( 1515)
  covalent geometry    : bond        0.00240 (11990)
  covalent geometry    : angle       0.48797 (16335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5003.56 seconds
wall clock time: 86 minutes 47.04 seconds (5207.04 seconds total)