Starting phenix.real_space_refine
on Wed Mar  4 06:18:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_25007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_25007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_25007.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_25007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sc0_25007/03_2026/7sc0_25007.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.039
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E, F, G, H, I, J, K
  Time building chain proxies: 1.44, per 1000 atoms: 0.12
  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: 0.66
  Conformation dependent library (CDL) restraints added in 497.4 milliseconds
  

  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: 0.34
  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: 1.50

  Time building geometry restraints manager: 0.91 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
}

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:             6.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.560
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.660
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG H 101 
 TYR   0.004   0.001   TYR I 148 
 PHE   0.006   0.001   PHE H 137 
 TRP   0.005   0.001   TRP E 128 
 HIS   0.001   0.000   HIS I 153 

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

*********************** 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  : 0.381 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1144
  time to fit residues: 23.2694
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  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.155168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.132233 restraints weight = 14430.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.89
r_work: 0.3454 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  11990  Z= 0.210
  Angle     :  0.633   5.404  16335  Z= 0.368
  Chirality :  0.047   0.139   1859
  Planarity :  0.004   0.031   1991
  Dihedral  :  4.420  16.228   1507
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.02 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  3.81 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.22), residues: 1397
  helix:  0.06 (0.18), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.14 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 171 
 TYR   0.008   0.001   TYR C 148 
 PHE   0.019   0.002   PHE H 107 
 TRP   0.005   0.001   TRP C  85 
 HIS   0.004   0.001   HIS I 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (11990)
  covalent geometry    : angle       0.63323 (16335)
  hydrogen bonds       : bond        0.11245 (  538)
  hydrogen bonds       : angle       4.10326 ( 1515)

*********************** 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
  167 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 0.346 
Fit side-chains
REVERT: I   61 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7627 (m-30)
  outliers start: 6
  outliers final: 2
  residues processed: 165
  average time/residue: 0.1065
  time to fit residues: 25.3186
Evaluate side-chains
  153 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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 117 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.159095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.137137 restraints weight = 14563.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.82
r_work: 0.3492 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2863

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= 0.176
  Angle     :  0.565   4.764  16335  Z= 0.324
  Chirality :  0.045   0.138   1859
  Planarity :  0.004   0.031   1991
  Dihedral  :  4.418  15.315   1507
  Min Nonbonded Distance : 2.676

Molprobity Statistics.
  All-atom Clashscore : 0.82
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.23 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  5.13 %
    Favored  : 92.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.23), residues: 1397
  helix:  0.40 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.22 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 101 
 TYR   0.009   0.001   TYR A 118 
 PHE   0.017   0.002   PHE C 137 
 TRP   0.005   0.001   TRP I 115 
 HIS   0.003   0.001   HIS C 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (11990)
  covalent geometry    : angle       0.56492 (16335)
  hydrogen bonds       : bond        0.09907 (  538)
  hydrogen bonds       : angle       3.84587 ( 1515)

*********************** 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
  185 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 156
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7742 (m-30)
  outliers start: 29
  outliers final: 23
  residues processed: 177
  average time/residue: 0.1066
  time to fit residues: 26.7545
Evaluate side-chains
  175 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
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  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  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  154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 128 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 114 optimal weight:    0.0370
   chunk 117 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0470
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.166693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.144924 restraints weight = 14236.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.83
r_work: 0.3586 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11990  Z= 0.129
  Angle     :  0.486   4.453  16335  Z= 0.276
  Chirality :  0.042   0.121   1859
  Planarity :  0.003   0.031   1991
  Dihedral  :  4.393  16.496   1507
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  5.67 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.23), residues: 1397
  helix:  0.53 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.18 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 101 
 TYR   0.006   0.001   TYR F 100 
 PHE   0.010   0.001   PHE G  89 
 TRP   0.008   0.001   TRP I 128 
 HIS   0.002   0.001   HIS H 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11990)
  covalent geometry    : angle       0.48635 (16335)
  hydrogen bonds       : bond        0.06741 (  538)
  hydrogen bonds       : angle       3.67720 ( 1515)

*********************** 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
  191 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.406 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7739 (m-30)
REVERT: I   61 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7539 (m-30)
  outliers start: 30
  outliers final: 17
  residues processed: 167
  average time/residue: 0.1167
  time to fit residues: 26.9597
Evaluate side-chains
  169 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   61 ASP
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 F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
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   69 GLU
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain K residue   61 ASP
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 20 optimal weight:    0.0040
   chunk 101 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 110 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0070
   chunk 52 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.2610

-------------------------------------------------------------------------------
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 = 0.4005 r_free = 0.4005 target = 0.170257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.149235 restraints weight = 14290.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.76
r_work: 0.3621 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11990  Z= 0.120
  Angle     :  0.474   4.665  16335  Z= 0.265
  Chirality :  0.041   0.121   1859
  Planarity :  0.003   0.031   1991
  Dihedral  :  4.200  15.661   1507
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  6.45 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.24), residues: 1397
  helix:  0.75 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.13 (0.25), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 101 
 TYR   0.006   0.001   TYR K 100 
 PHE   0.008   0.001   PHE C  89 
 TRP   0.005   0.001   TRP G  98 
 HIS   0.002   0.000   HIS B 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11990)
  covalent geometry    : angle       0.47355 (16335)
  hydrogen bonds       : bond        0.06472 (  538)
  hydrogen bonds       : angle       3.55232 ( 1515)

*********************** 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
  194 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.415 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7765 (t0)
REVERT: C   49 ILE cc_start: 0.7378 (mm) cc_final: 0.6705 (mm)
REVERT: I   61 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (m-30)
REVERT: J  175 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6534 (pt0)
  outliers start: 33
  outliers final: 15
  residues processed: 171
  average time/residue: 0.1205
  time to fit residues: 27.9011
Evaluate side-chains
  166 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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  175 GLN
Chi-restraints excluded: chain C residue   61 ASP
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 F residue   59 LEU
Chi-restraints excluded: chain F residue   61 ASP
Chi-restraints excluded: chain F residue   69 GLU
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue   69 GLU
Chi-restraints excluded: chain H residue   69 GLU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain J residue  175 GLN
Chi-restraints excluded: chain K residue   59 LEU
Chi-restraints excluded: chain K residue   61 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 127 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 86 optimal weight:    0.3980
   chunk 115 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.165875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.144934 restraints weight = 14391.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.73
r_work: 0.3581 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3561

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= 0.135
  Angle     :  0.495   4.534  16335  Z= 0.279
  Chirality :  0.042   0.127   1859
  Planarity :  0.003   0.030   1991
  Dihedral  :  4.117  14.945   1507
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 0.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  7.77 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.004   0.000   ARG K 101 
 TYR   0.006   0.001   TYR H 148 
 PHE   0.011   0.001   PHE J  81 
 TRP   0.003   0.000   TRP B 128 
 HIS   0.002   0.000   HIS J 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11990)
  covalent geometry    : angle       0.49489 (16335)
  hydrogen bonds       : bond        0.07362 (  538)
  hydrogen bonds       : angle       3.60314 ( 1515)

*********************** 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
  172 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.423 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7817 (t0)
REVERT: E   61 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7831 (m-30)
REVERT: I   61 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7593 (m-30)
  outliers start: 24
  outliers final: 9
  residues processed: 154
  average time/residue: 0.1197
  time to fit residues: 25.7187
Evaluate side-chains
  158 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain B residue   61 ASP
Chi-restraints excluded: chain C residue   61 ASP
Chi-restraints excluded: chain D residue   61 ASP
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 G residue   61 ASP
Chi-restraints excluded: chain H residue   69 GLU
Chi-restraints excluded: chain I residue   61 ASP
Chi-restraints excluded: chain I residue   69 GLU
Chi-restraints excluded: chain K residue   61 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.158102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.137646 restraints weight = 14277.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.63
r_work: 0.3512 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11990  Z= 0.162
  Angle     :  0.540   4.651  16335  Z= 0.308
  Chirality :  0.043   0.139   1859
  Planarity :  0.003   0.028   1991
  Dihedral  :  4.218  15.084   1507
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 0.90
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 11.31 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  7.77 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.24), residues: 1397
  helix:  0.81 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.22 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 101 
 TYR   0.009   0.001   TYR A  97 
 PHE   0.016   0.002   PHE C 137 
 TRP   0.004   0.001   TRP I 128 
 HIS   0.003   0.001   HIS J 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11990)
  covalent geometry    : angle       0.54029 (16335)
  hydrogen bonds       : bond        0.08934 (  538)
  hydrogen bonds       : angle       3.74644 ( 1515)

*********************** 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
  186 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.454 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7852 (m-30)
REVERT: G   49 ILE cc_start: 0.7396 (mm) cc_final: 0.6769 (mm)
REVERT: H   49 ILE cc_start: 0.7382 (mm) cc_final: 0.6892 (mm)
REVERT: I   61 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7736 (m-30)
  outliers start: 29
  outliers final: 17
  residues processed: 164
  average time/residue: 0.1098
  time to fit residues: 25.4704
Evaluate side-chains
  174 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  154 THR
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 G residue   61 ASP
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 K residue   61 ASP
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 106 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.158898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138447 restraints weight = 14275.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.63
r_work: 0.3538 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3676

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= 0.155
  Angle     :  0.524   4.625  16335  Z= 0.299
  Chirality :  0.043   0.134   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.238  15.534   1507
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 0.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.09 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  8.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.24), residues: 1397
  helix:  0.84 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.25 (0.24), residues: 561

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11990)
  covalent geometry    : angle       0.52394 (16335)
  hydrogen bonds       : bond        0.08447 (  538)
  hydrogen bonds       : angle       3.70581 ( 1515)

*********************** 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
  191 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.443 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7902 (m-30)
REVERT: G   49 ILE cc_start: 0.7425 (mm) cc_final: 0.6790 (mm)
REVERT: H   49 ILE cc_start: 0.7386 (mm) cc_final: 0.6965 (mm)
REVERT: I   49 ILE cc_start: 0.7589 (mm) cc_final: 0.7152 (mm)
REVERT: I   61 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7689 (m-30)
  outliers start: 33
  outliers final: 23
  residues processed: 167
  average time/residue: 0.1082
  time to fit residues: 25.4903
Evaluate side-chains
  183 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 158
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  154 THR
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   59 LEU
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue  154 THR
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   59 LEU
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 50 optimal weight:    0.1980
   chunk 103 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 101 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.160570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.140160 restraints weight = 14038.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.63
r_work: 0.3547 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11990  Z= 0.139
  Angle     :  0.505   4.570  16335  Z= 0.286
  Chirality :  0.042   0.127   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.243  15.603   1507
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.81 %
    Favored  : 89.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  8.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.24), residues: 1397
  helix:  0.93 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.24 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 101 
 TYR   0.014   0.001   TYR G  97 
 PHE   0.014   0.001   PHE J  81 
 TRP   0.003   0.000   TRP H  98 
 HIS   0.002   0.000   HIS H 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11990)
  covalent geometry    : angle       0.50484 (16335)
  hydrogen bonds       : bond        0.07702 (  538)
  hydrogen bonds       : angle       3.67517 ( 1515)

*********************** 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
  191 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.331 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7885 (m-30)
REVERT: G   49 ILE cc_start: 0.7459 (mm) cc_final: 0.6814 (mm)
REVERT: I   61 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7693 (m-30)
  outliers start: 31
  outliers final: 22
  residues processed: 167
  average time/residue: 0.1063
  time to fit residues: 24.9126
Evaluate side-chains
  183 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   61 ASP
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 G residue   59 LEU
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue  154 THR
Chi-restraints excluded: chain H residue   61 ASP
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   59 LEU
Chi-restraints excluded: chain J residue   61 ASP
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0980
   chunk 10 optimal weight:    0.2980
   chunk 74 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.161171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.140686 restraints weight = 14201.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 1.63
r_work: 0.3571 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3877

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     :  0.501   4.518  16335  Z= 0.284
  Chirality :  0.042   0.128   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.192  15.625   1507
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.24), residues: 1397
  helix:  0.98 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.23 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 101 
 TYR   0.010   0.001   TYR E  97 
 PHE   0.014   0.001   PHE J  81 
 TRP   0.007   0.000   TRP K  98 
 HIS   0.002   0.000   HIS J 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11990)
  covalent geometry    : angle       0.50149 (16335)
  hydrogen bonds       : bond        0.07568 (  538)
  hydrogen bonds       : angle       3.64328 ( 1515)

********************** 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
  184 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.327 
Fit side-chains
REVERT: E   61 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7925 (m-30)
REVERT: G   49 ILE cc_start: 0.7575 (mm) cc_final: 0.7324 (mt)
REVERT: I   61 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7671 (m-30)
  outliers start: 26
  outliers final: 24
  residues processed: 165
  average time/residue: 0.1119
  time to fit residues: 25.8975
Evaluate side-chains
  181 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASP
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   61 ASP
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   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 G residue   59 LEU
Chi-restraints excluded: chain G residue   61 ASP
Chi-restraints excluded: chain G residue  154 THR
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   59 LEU
Chi-restraints excluded: chain K residue   61 ASP
Chi-restraints excluded: chain K residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0980
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.161537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.141090 restraints weight = 14110.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.62
r_work: 0.3557 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3926

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= 0.134
  Angle     :  0.500   4.533  16335  Z= 0.282
  Chirality :  0.042   0.128   1859
  Planarity :  0.003   0.029   1991
  Dihedral  :  4.194  15.644   1507
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  8.39 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.24), residues: 1397
  helix:  1.00 (0.19), residues: 836
  sheet:  None (None), residues: 0
  loop : -3.22 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 101 
 TYR   0.008   0.001   TYR F  97 
 PHE   0.014   0.001   PHE J  81 
 TRP   0.007   0.000   TRP K  98 
 HIS   0.002   0.000   HIS J 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11990)
  covalent geometry    : angle       0.49962 (16335)
  hydrogen bonds       : bond        0.07448 (  538)
  hydrogen bonds       : angle       3.64082 ( 1515)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2183.24 seconds
wall clock time: 38 minutes 10.08 seconds (2290.08 seconds total)