Starting phenix.real_space_refine
on Mon Jun 16 05:42:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f3e_31432/06_2025/7f3e_31432.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      84      5.16       5
     C   11868      2.51       5
     N    3168      2.21       5
     O    3444      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 18564
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1547
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 5.63, per 1000 atoms: 0.30
  Number of scatterers: 18564
  At special positions: 0
  Unit cell: (102.96, 157.52, 136.4, 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      84     16.00
     O    3444      8.00
     N    3168      7.00
     C   11868      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: 4.59
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4296

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 18 sheets defined
      70.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'E' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL E  10 " --> pdb=" O   ASP E   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE E  11 " --> pdb=" O   THR E   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 7 through 11'
    Processing helix  chain 'E' and resid 13 through 20
    Processing helix  chain 'E' and resid 26 through 37
      removed outlier: 3.741A  pdb=" N   ASN E  37 " --> pdb=" O   HIS E  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
    Processing helix  chain 'E' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE E  65 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR E  95 " --> pdb=" O   GLU E  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 116 through 133
    Processing helix  chain 'E' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL E 143 " --> pdb=" O   SER E 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU E 152 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR E 165 " --> pdb=" O   GLU E 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP E 166 " --> pdb=" O   GLY E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 190
    Processing helix  chain 'F' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL F  10 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE F  11 " --> pdb=" O   THR F   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 7 through 11'
    Processing helix  chain 'F' and resid 13 through 20
    Processing helix  chain 'F' and resid 26 through 37
      removed outlier: 3.741A  pdb=" N   ASN F  37 " --> pdb=" O   HIS F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 46 through 56
    Processing helix  chain 'F' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE F  65 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR F  95 " --> pdb=" O   GLU F  91 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 116 through 133
    Processing helix  chain 'F' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL F 143 " --> pdb=" O   SER F 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU F 152 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR F 165 " --> pdb=" O   GLU F 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP F 166 " --> pdb=" O   GLY F 162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 190
    Processing helix  chain 'C' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL C  10 " --> pdb=" O   ASP C   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE C  11 " --> pdb=" O   THR C   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 7 through 11'
    Processing helix  chain 'C' and resid 13 through 20
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.743A  pdb=" N   ASN C  37 " --> pdb=" O   HIS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 56
    Processing helix  chain 'C' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE C  65 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 133
    Processing helix  chain 'C' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU C 152 " --> pdb=" O   LEU C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR C 165 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP C 166 " --> pdb=" O   GLY C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 190
    Processing helix  chain 'D' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL D  10 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE D  11 " --> pdb=" O   THR D   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 7 through 11'
    Processing helix  chain 'D' and resid 13 through 20
    Processing helix  chain 'D' and resid 26 through 37
      removed outlier: 3.740A  pdb=" N   ASN D  37 " --> pdb=" O   HIS D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 56
    Processing helix  chain 'D' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE D  65 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 114
      removed outlier: 3.837A  pdb=" N   TYR D  95 " --> pdb=" O   GLU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 116 through 133
    Processing helix  chain 'D' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL D 143 " --> pdb=" O   SER D 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR D 165 " --> pdb=" O   GLU D 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP D 166 " --> pdb=" O   GLY D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 190
    Processing helix  chain 'A' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL A  10 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE A  11 " --> pdb=" O   THR A   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 7 through 11'
    Processing helix  chain 'A' and resid 13 through 20
    Processing helix  chain 'A' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN A  37 " --> pdb=" O   HIS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
    Processing helix  chain 'A' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 114
      removed outlier: 3.839A  pdb=" N   TYR A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 133
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL A 143 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 190
    Processing helix  chain 'B' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL B  10 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE B  11 " --> pdb=" O   THR B   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 7 through 11'
    Processing helix  chain 'B' and resid 13 through 20
    Processing helix  chain 'B' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN B  37 " --> pdb=" O   HIS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 56
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.872A  pdb=" N   PHE B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR B  95 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 133
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 4.014A  pdb=" N   VAL B 143 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR B 165 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP B 166 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 190
    Processing helix  chain 'H' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL H  10 " --> pdb=" O   ASP H   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE H  11 " --> pdb=" O   THR H   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 7 through 11'
    Processing helix  chain 'H' and resid 13 through 20
    Processing helix  chain 'H' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN H  37 " --> pdb=" O   HIS H  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 56
    Processing helix  chain 'H' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE H  65 " --> pdb=" O   LEU H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 114
      removed outlier: 3.837A  pdb=" N   TYR H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 133
    Processing helix  chain 'H' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL H 143 " --> pdb=" O   SER H 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU H 152 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR H 165 " --> pdb=" O   GLU H 161 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   TRP H 166 " --> pdb=" O   GLY H 162 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 179 through 190
    Processing helix  chain 'G' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL G  10 " --> pdb=" O   ASP G   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE G  11 " --> pdb=" O   THR G   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 7 through 11'
    Processing helix  chain 'G' and resid 13 through 20
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN G  37 " --> pdb=" O   HIS G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 56
    Processing helix  chain 'G' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE G  65 " --> pdb=" O   LEU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 116 through 133
    Processing helix  chain 'G' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL G 143 " --> pdb=" O   SER G 139 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU G 152 " --> pdb=" O   LEU G 148 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 160 through 171
      removed outlier: 4.164A  pdb=" N   THR G 165 " --> pdb=" O   GLU G 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP G 166 " --> pdb=" O   GLY G 162 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 179 through 190
    Processing helix  chain 'J' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL J  10 " --> pdb=" O   ASP J   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE J  11 " --> pdb=" O   THR J   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 7 through 11'
    Processing helix  chain 'J' and resid 13 through 20
    Processing helix  chain 'J' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN J  37 " --> pdb=" O   HIS J  33 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 46 through 56
    Processing helix  chain 'J' and resid 61 through 68
      removed outlier: 3.873A  pdb=" N   PHE J  65 " --> pdb=" O   LEU J  61 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR J  95 " --> pdb=" O   GLU J  91 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 133
    Processing helix  chain 'J' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL J 143 " --> pdb=" O   SER J 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU J 152 " --> pdb=" O   LEU J 148 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR J 165 " --> pdb=" O   GLU J 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP J 166 " --> pdb=" O   GLY J 162 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 179 through 190
    Processing helix  chain 'I' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL I  10 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE I  11 " --> pdb=" O   THR I   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 7 through 11'
    Processing helix  chain 'I' and resid 13 through 20
    Processing helix  chain 'I' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN I  37 " --> pdb=" O   HIS I  33 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 46 through 56
    Processing helix  chain 'I' and resid 61 through 68
      removed outlier: 3.872A  pdb=" N   PHE I  65 " --> pdb=" O   LEU I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 83 through 114
      removed outlier: 3.838A  pdb=" N   TYR I  95 " --> pdb=" O   GLU I  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 116 through 133
    Processing helix  chain 'I' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL I 143 " --> pdb=" O   SER I 139 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU I 152 " --> pdb=" O   LEU I 148 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR I 165 " --> pdb=" O   GLU I 161 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TRP I 166 " --> pdb=" O   GLY I 162 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 179 through 190
    Processing helix  chain 'L' and resid 7 through 11
      removed outlier: 3.970A  pdb=" N   VAL L  10 " --> pdb=" O   ASP L   7 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE L  11 " --> pdb=" O   THR L   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 7 through 11'
    Processing helix  chain 'L' and resid 13 through 20
    Processing helix  chain 'L' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN L  37 " --> pdb=" O   HIS L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 56
    Processing helix  chain 'L' and resid 61 through 68
      removed outlier: 3.875A  pdb=" N   PHE L  65 " --> pdb=" O   LEU L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 83 through 114
      removed outlier: 3.840A  pdb=" N   TYR L  95 " --> pdb=" O   GLU L  91 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 116 through 133
    Processing helix  chain 'L' and resid 139 through 152
      removed outlier: 4.013A  pdb=" N   VAL L 143 " --> pdb=" O   SER L 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU L 152 " --> pdb=" O   LEU L 148 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 160 through 171
      removed outlier: 4.166A  pdb=" N   THR L 165 " --> pdb=" O   GLU L 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP L 166 " --> pdb=" O   GLY L 162 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 179 through 190
    Processing helix  chain 'K' and resid 7 through 11
      removed outlier: 3.969A  pdb=" N   VAL K  10 " --> pdb=" O   ASP K   7 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE K  11 " --> pdb=" O   THR K   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 7 through 11'
    Processing helix  chain 'K' and resid 13 through 20
    Processing helix  chain 'K' and resid 26 through 37
      removed outlier: 3.742A  pdb=" N   ASN K  37 " --> pdb=" O   HIS K  33 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 46 through 56
    Processing helix  chain 'K' and resid 61 through 68
      removed outlier: 3.874A  pdb=" N   PHE K  65 " --> pdb=" O   LEU K  61 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 83 through 114
      removed outlier: 3.839A  pdb=" N   TYR K  95 " --> pdb=" O   GLU K  91 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 116 through 133
    Processing helix  chain 'K' and resid 139 through 152
      removed outlier: 4.012A  pdb=" N   VAL K 143 " --> pdb=" O   SER K 139 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU K 152 " --> pdb=" O   LEU K 148 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 160 through 171
      removed outlier: 4.165A  pdb=" N   THR K 165 " --> pdb=" O   GLU K 161 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TRP K 166 " --> pdb=" O   GLY K 162 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 179 through 190
    Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS E  70 " --> pdb=" O   PHE E  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE E   4 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82
    Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS F  70 " --> pdb=" O   PHE F  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE F   4 " --> pdb=" O   TYR F  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS C  70 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE C   4 " --> pdb=" O   TYR C  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82
    Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS D  70 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE D   4 " --> pdb=" O   TYR D  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS A  70 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE A   4 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82
    Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS B  70 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE B   4 " --> pdb=" O   TYR B  43 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS H  70 " --> pdb=" O   PHE H  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE H   4 " --> pdb=" O   TYR H  43 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 82
    Processing sheet with id=AB3, first strand: chain 'G' and resid 69 through 72
      removed outlier: 3.862A  pdb=" N   LYS G  70 " --> pdb=" O   PHE G  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE G   4 " --> pdb=" O   TYR G  43 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS J  70 " --> pdb=" O   PHE J  42 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   PHE J   4 " --> pdb=" O   TYR J  43 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'J' and resid 80 through 82
    Processing sheet with id=AB6, first strand: chain 'I' and resid 69 through 72
      removed outlier: 3.860A  pdb=" N   LYS I  70 " --> pdb=" O   PHE I  42 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   PHE I   4 " --> pdb=" O   TYR I  43 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS L  70 " --> pdb=" O   PHE L  42 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   PHE L   4 " --> pdb=" O   TYR L  43 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 82
    Processing sheet with id=AB9, first strand: chain 'K' and resid 69 through 72
      removed outlier: 3.861A  pdb=" N   LYS K  70 " --> pdb=" O   PHE K  42 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   PHE K   4 " --> pdb=" O   TYR K  43 " (cutoff:3.500A)

    1056 hydrogen bonds defined for protein.
    3168 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: 5.92

  Time building geometry restraints manager: 5.44 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: 6156
        1.34 -     1.46: 3204
        1.46 -     1.57: 9372
        1.57 -     1.69: 0
        1.69 -     1.81: 156
  Bond restraints: 18888
  Sorted by residual:
  bond pdb=" CB  VAL L 143 "
       pdb=" CG2 VAL L 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CG1 ILE I  90 "
       pdb=" CD1 ILE I  90 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.03e+00
  bond pdb=" CB  VAL C 143 "
       pdb=" CG2 VAL C 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  bond pdb=" CG1 ILE K  90 "
       pdb=" CD1 ILE K  90 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  bond pdb=" CB  VAL B 143 "
       pdb=" CG2 VAL B 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  ... (remaining 18883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 22717
        1.04 -     2.07: 2273
        2.07 -     3.11: 278
        3.11 -     4.14: 105
        4.14 -     5.18: 55
  Bond angle restraints: 25428
  Sorted by residual:
  angle pdb=" N   THR K  12 "
        pdb=" CA  THR K  12 "
        pdb=" C   THR K  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.72    2.84 1.27e+00 6.20e-01 4.98e+00
  angle pdb=" N   THR I  12 "
        pdb=" CA  THR I  12 "
        pdb=" C   THR I  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.76    2.80 1.27e+00 6.20e-01 4.87e+00
  angle pdb=" N   THR L  12 "
        pdb=" CA  THR L  12 "
        pdb=" C   THR L  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.76    2.80 1.27e+00 6.20e-01 4.85e+00
  angle pdb=" N   GLU I  60 "
        pdb=" CA  GLU I  60 "
        pdb=" CB  GLU I  60 "
      ideal   model   delta    sigma   weight residual
     113.65  110.42    3.23 1.47e+00 4.63e-01 4.83e+00
  angle pdb=" N   THR E  12 "
        pdb=" CA  THR E  12 "
        pdb=" C   THR E  12 "
      ideal   model   delta    sigma   weight residual
     114.56  111.77    2.79 1.27e+00 6.20e-01 4.82e+00
  ... (remaining 25423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 9739
       14.72 -    29.44: 1301
       29.44 -    44.16: 312
       44.16 -    58.88: 108
       58.88 -    73.60: 48
  Dihedral angle restraints: 11508
    sinusoidal: 4896
      harmonic: 6612
  Sorted by residual:
  dihedral pdb=" CA  PHE B  11 "
           pdb=" C   PHE B  11 "
           pdb=" N   THR B  12 "
           pdb=" CA  THR B  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.64   21.36     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  PHE J  11 "
           pdb=" C   PHE J  11 "
           pdb=" N   THR J  12 "
           pdb=" CA  THR J  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  PHE E  11 "
           pdb=" C   PHE E  11 "
           pdb=" N   THR E  12 "
           pdb=" CA  THR E  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.67   21.33     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 11505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1706
       0.033 -    0.066: 747
       0.066 -    0.099: 242
       0.099 -    0.131: 101
       0.131 -    0.164: 36
  Chirality restraints: 2832
  Sorted by residual:
  chirality pdb=" CB  ILE F  16 "
            pdb=" CA  ILE F  16 "
            pdb=" CG1 ILE F  16 "
            pdb=" CG2 ILE F  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE C  16 "
            pdb=" CA  ILE C  16 "
            pdb=" CG1 ILE C  16 "
            pdb=" CG2 ILE C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CB  ILE G  16 "
            pdb=" CA  ILE G  16 "
            pdb=" CG1 ILE G  16 "
            pdb=" CG2 ILE G  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 2829 not shown)

  Planarity restraints: 3252
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G  73 "   -0.039 5.00e-02 4.00e+02   5.89e-02 5.56e+00
        pdb=" N   PRO G  74 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO G  74 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO G  74 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F  73 "    0.038 5.00e-02 4.00e+02   5.88e-02 5.54e+00
        pdb=" N   PRO F  74 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO F  74 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO F  74 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  73 "    0.038 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO D  74 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D  74 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  74 "    0.033 5.00e-02 4.00e+02
  ... (remaining 3249 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3704
        2.77 -     3.30: 18450
        3.30 -     3.84: 29189
        3.84 -     4.37: 34003
        4.37 -     4.90: 58577
  Nonbonded interactions: 143923
  Sorted by model distance:
  nonbonded pdb=" O   GLU K 105 "
            pdb=" OG1 THR K 108 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   GLU B 105 "
            pdb=" OG1 THR B 108 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   GLU D 105 "
            pdb=" OG1 THR D 108 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU J 105 "
            pdb=" OG1 THR J 108 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU A 105 "
            pdb=" OG1 THR A 108 "
     model   vdw
     2.243 3.040
  ... (remaining 143918 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.780
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     36.200
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
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      :  0.005   0.040  18888  Z= 0.217
  Angle     :  0.709   5.179  25428  Z= 0.426
  Chirality :  0.045   0.164   2832
  Planarity :  0.005   0.059   3252
  Dihedral  : 15.180  73.599   7212
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.17), residues: 2208
  helix:  0.86 (0.14), residues: 1428
  sheet:  None (None), residues: 0
  loop : -2.50 (0.18), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 166 
 HIS   0.002   0.001   HIS J  33 
 PHE   0.014   0.002   PHE A  31 
 TYR   0.012   0.002   TYR B 128 
 ARG   0.007   0.001   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18845 ( 1056)
  hydrogen bonds       : angle       6.16552 ( 3168)
  covalent geometry    : bond        0.00513 (18888)
  covalent geometry    : angle       0.70889 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 453
  time to evaluate  : 2.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   13 ASN cc_start: 0.5555 (t0) cc_final: 0.5293 (m-40)
REVERT: C   51 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6167 (mm-30)
REVERT: D   55 ILE cc_start: 0.7123 (mt) cc_final: 0.6551 (mt)
REVERT: D  160 ASP cc_start: 0.7527 (t70) cc_final: 0.6261 (m-30)
REVERT: J   13 ASN cc_start: 0.5631 (t0) cc_final: 0.5373 (m-40)
REVERT: J   51 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6178 (mm-30)
REVERT: J   98 ASN cc_start: 0.7757 (m-40) cc_final: 0.7534 (m-40)
REVERT: I   55 ILE cc_start: 0.7212 (mt) cc_final: 0.6674 (mt)
REVERT: I  160 ASP cc_start: 0.7614 (t70) cc_final: 0.6345 (m-30)
REVERT: L  160 ASP cc_start: 0.5787 (t70) cc_final: 0.5510 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 453
  average time/residue: 0.3171
  time to fit residues: 213.1195
Evaluate side-chains
  255 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 2.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    6.9990
   chunk 163 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 169 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 102 optimal weight:    0.5980
   chunk 126 optimal weight:    4.9990
   chunk 196 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
J 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.237386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.219989 restraints weight = 22236.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.202416 restraints weight = 31973.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.201710 restraints weight = 28024.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  18888  Z= 0.146
  Angle     :  0.604   6.341  25428  Z= 0.330
  Chirality :  0.044   0.138   2832
  Planarity :  0.005   0.050   3252
  Dihedral  :  4.533  21.501   2520
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.63 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.17), residues: 2208
  helix:  0.87 (0.13), residues: 1500
  sheet: -1.72 (0.47), residues: 120
  loop : -2.82 (0.20), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L 166 
 HIS   0.003   0.001   HIS J 190 
 PHE   0.018   0.002   PHE A  77 
 TYR   0.026   0.001   TYR K  87 
 ARG   0.006   0.001   ARG H 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05273 ( 1056)
  hydrogen bonds       : angle       4.28725 ( 3168)
  covalent geometry    : bond        0.00334 (18888)
  covalent geometry    : angle       0.60389 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 293
  time to evaluate  : 2.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    7 ASP cc_start: 0.6598 (t70) cc_final: 0.6167 (t0)
REVERT: F   56 MET cc_start: 0.7398 (tmm) cc_final: 0.7109 (tmm)
REVERT: C   13 ASN cc_start: 0.6011 (t0) cc_final: 0.5763 (m-40)
REVERT: C   67 MET cc_start: 0.5462 (mmm) cc_final: 0.5003 (mpp)
REVERT: D   51 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7730 (mt-10)
REVERT: A   56 MET cc_start: 0.6304 (ttt) cc_final: 0.6100 (ttm)
REVERT: B   56 MET cc_start: 0.4733 (ppp) cc_final: 0.4527 (ppp)
REVERT: G   56 MET cc_start: 0.7383 (tmm) cc_final: 0.7093 (tmm)
REVERT: J   13 ASN cc_start: 0.6150 (t0) cc_final: 0.5832 (m-40)
REVERT: J   98 ASN cc_start: 0.7816 (m-40) cc_final: 0.7451 (m110)
REVERT: L  160 ASP cc_start: 0.6173 (t70) cc_final: 0.5499 (m-30)
REVERT: K    1 MET cc_start: 0.1348 (tpt) cc_final: 0.0985 (tpt)
REVERT: K  129 ARG cc_start: 0.5767 (ttp80) cc_final: 0.5566 (tmm160)
  outliers start: 19
  outliers final: 17
  residues processed: 303
  average time/residue: 0.3112
  time to fit residues: 142.3068
Evaluate side-chains
  251 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 2.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue  168 ASP
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 186 optimal weight:    9.9990
   chunk 174 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 151 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0970
   chunk 99 optimal weight:   10.0000
   chunk 134 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 150 optimal weight:    1.9990
   chunk 185 optimal weight:    6.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
C 190 HIS
J 179 ASN
J 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.239787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.226837 restraints weight = 22142.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.209175 restraints weight = 32892.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.206508 restraints weight = 33771.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18888  Z= 0.138
  Angle     :  0.569   6.413  25428  Z= 0.309
  Chirality :  0.043   0.152   2832
  Planarity :  0.004   0.043   3252
  Dihedral  :  4.376  20.430   2520
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.97 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.18), residues: 2208
  helix:  1.08 (0.14), residues: 1488
  sheet: -1.77 (0.44), residues: 120
  loop : -2.79 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 166 
 HIS   0.009   0.001   HIS F  33 
 PHE   0.027   0.002   PHE J  11 
 TYR   0.016   0.001   TYR K  87 
 ARG   0.006   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04778 ( 1056)
  hydrogen bonds       : angle       4.07260 ( 3168)
  covalent geometry    : bond        0.00324 (18888)
  covalent geometry    : angle       0.56865 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 253
  time to evaluate  : 2.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4677 (OUTLIER) cc_final: 0.4289 (p90)
REVERT: E  105 GLU cc_start: 0.5352 (tt0) cc_final: 0.5150 (tt0)
REVERT: F    7 ASP cc_start: 0.6339 (t70) cc_final: 0.6125 (t0)
REVERT: D   51 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7593 (mt-10)
REVERT: D   64 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5561 (mm-30)
REVERT: D  178 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6695 (mppt)
REVERT: A   56 MET cc_start: 0.6209 (ttt) cc_final: 0.6009 (ttm)
REVERT: A   62 TRP cc_start: 0.5637 (m100) cc_final: 0.4823 (m100)
REVERT: A   80 THR cc_start: 0.7316 (p) cc_final: 0.6719 (t)
REVERT: B   52 MET cc_start: 0.7343 (tmm) cc_final: 0.7031 (ttp)
REVERT: B   67 MET cc_start: 0.6371 (tpp) cc_final: 0.6112 (ttt)
REVERT: B  153 ASP cc_start: 0.7251 (m-30) cc_final: 0.6997 (m-30)
REVERT: G  133 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.7968 (mtp85)
REVERT: J   98 ASN cc_start: 0.7794 (m-40) cc_final: 0.7441 (m-40)
REVERT: L   80 THR cc_start: 0.7155 (p) cc_final: 0.6559 (t)
REVERT: L  160 ASP cc_start: 0.6121 (t70) cc_final: 0.5667 (m-30)
REVERT: K    1 MET cc_start: 0.1425 (tpt) cc_final: 0.1073 (pmm)
  outliers start: 49
  outliers final: 30
  residues processed: 287
  average time/residue: 0.2924
  time to fit residues: 130.8739
Evaluate side-chains
  258 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 225
  time to evaluate  : 2.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  169 LYS
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 85 optimal weight:    0.0020
   chunk 123 optimal weight:    2.9990
   chunk 198 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 195 optimal weight:    9.9990
   chunk 110 optimal weight:    8.9990
   chunk 98 optimal weight:    2.9990
   chunk 155 optimal weight:    7.9990
   chunk 162 optimal weight:    6.9990
   chunk 204 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    2.7996

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
D 179 ASN
A 179 ASN
J 179 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.231992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.217588 restraints weight = 22151.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.199862 restraints weight = 34290.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.199362 restraints weight = 37694.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  18888  Z= 0.224
  Angle     :  0.664   7.098  25428  Z= 0.357
  Chirality :  0.047   0.140   2832
  Planarity :  0.005   0.039   3252
  Dihedral  :  4.840  23.400   2520
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.11 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.18), residues: 2208
  helix:  0.86 (0.13), residues: 1488
  sheet: -1.52 (0.55), residues: 120
  loop : -2.70 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  62 
 HIS   0.008   0.001   HIS G  33 
 PHE   0.035   0.003   PHE H  31 
 TYR   0.020   0.002   TYR K  87 
 ARG   0.009   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05900 ( 1056)
  hydrogen bonds       : angle       4.33425 ( 3168)
  covalent geometry    : bond        0.00559 (18888)
  covalent geometry    : angle       0.66445 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 236
  time to evaluate  : 2.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4351 (p90)
REVERT: F    7 ASP cc_start: 0.6540 (t70) cc_final: 0.6325 (t0)
REVERT: C  151 GLU cc_start: 0.6375 (pt0) cc_final: 0.5952 (tt0)
REVERT: D   51 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7204 (mp0)
REVERT: D   64 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5865 (mm-30)
REVERT: D  178 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6953 (mppt)
REVERT: A   80 THR cc_start: 0.7391 (p) cc_final: 0.6851 (t)
REVERT: B   52 MET cc_start: 0.7427 (tmm) cc_final: 0.6431 (ttt)
REVERT: J   98 ASN cc_start: 0.7853 (m-40) cc_final: 0.7611 (m-40)
REVERT: L   80 THR cc_start: 0.7320 (p) cc_final: 0.6769 (t)
REVERT: L  160 ASP cc_start: 0.6372 (t70) cc_final: 0.5866 (m-30)
REVERT: K    1 MET cc_start: 0.1660 (tpt) cc_final: 0.1302 (pmm)
  outliers start: 77
  outliers final: 47
  residues processed: 290
  average time/residue: 0.2825
  time to fit residues: 128.3716
Evaluate side-chains
  269 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 219
  time to evaluate  : 2.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue    9 SER
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue    7 ASP
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue    9 SER
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   37 ASN
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  169 LYS
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 158 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 215 optimal weight:    0.5980
   chunk 180 optimal weight:    9.9990
   chunk 143 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 165 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
D 179 ASN
A 179 ASN
J 179 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.237843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.224731 restraints weight = 22154.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 86)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.205126 restraints weight = 33519.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.204285 restraints weight = 30698.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18888  Z= 0.130
  Angle     :  0.542   6.583  25428  Z= 0.295
  Chirality :  0.042   0.123   2832
  Planarity :  0.004   0.035   3252
  Dihedral  :  4.358  21.830   2520
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.41 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.18), residues: 2208
  helix:  1.04 (0.14), residues: 1488
  sheet: -2.07 (0.38), residues: 120
  loop : -2.69 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 166 
 HIS   0.009   0.001   HIS F  33 
 PHE   0.020   0.001   PHE J  11 
 TYR   0.023   0.001   TYR K  87 
 ARG   0.005   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04475 ( 1056)
  hydrogen bonds       : angle       4.04171 ( 3168)
  covalent geometry    : bond        0.00301 (18888)
  covalent geometry    : angle       0.54211 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 242
  time to evaluate  : 2.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4804 (OUTLIER) cc_final: 0.4176 (p90)
REVERT: F    7 ASP cc_start: 0.6364 (t70) cc_final: 0.6152 (t0)
REVERT: C  151 GLU cc_start: 0.6258 (pt0) cc_final: 0.5854 (tt0)
REVERT: D   51 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7083 (mp0)
REVERT: D   64 GLU cc_start: 0.6357 (mm-30) cc_final: 0.5901 (mm-30)
REVERT: A   80 THR cc_start: 0.7343 (p) cc_final: 0.6802 (t)
REVERT: B   52 MET cc_start: 0.7179 (tmm) cc_final: 0.6383 (ttt)
REVERT: B   67 MET cc_start: 0.7377 (tmm) cc_final: 0.6942 (ttp)
REVERT: J   98 ASN cc_start: 0.7821 (m-40) cc_final: 0.7613 (m-40)
REVERT: L   80 THR cc_start: 0.7284 (p) cc_final: 0.6782 (t)
REVERT: L  160 ASP cc_start: 0.6493 (t70) cc_final: 0.5819 (m-30)
REVERT: K    1 MET cc_start: 0.1411 (tpt) cc_final: 0.0913 (pmm)
  outliers start: 69
  outliers final: 50
  residues processed: 287
  average time/residue: 0.2872
  time to fit residues: 129.5620
Evaluate side-chains
  269 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 217
  time to evaluate  : 2.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   37 ASN
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   19 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 LEU
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  108 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   19 THR
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   67 MET
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 211 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 175 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   chunk 139 optimal weight:    0.3980
   chunk 171 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
J 179 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.238650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.225542 restraints weight = 22097.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.208164 restraints weight = 32795.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.206164 restraints weight = 24711.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18888  Z= 0.127
  Angle     :  0.533   6.337  25428  Z= 0.291
  Chirality :  0.042   0.124   2832
  Planarity :  0.004   0.039   3252
  Dihedral  :  4.257  21.541   2520
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.36 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.18), residues: 2208
  helix:  1.07 (0.14), residues: 1488
  sheet: -2.19 (0.35), residues: 120
  loop : -2.58 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  62 
 HIS   0.009   0.001   HIS G  33 
 PHE   0.019   0.001   PHE J  11 
 TYR   0.028   0.001   TYR K  87 
 ARG   0.006   0.000   ARG H 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 ( 1056)
  hydrogen bonds       : angle       3.98603 ( 3168)
  covalent geometry    : bond        0.00292 (18888)
  covalent geometry    : angle       0.53304 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 224
  time to evaluate  : 2.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.4136 (p90)
REVERT: E  105 GLU cc_start: 0.5402 (tt0) cc_final: 0.5088 (tt0)
REVERT: F    7 ASP cc_start: 0.6388 (t70) cc_final: 0.6181 (t0)
REVERT: C  151 GLU cc_start: 0.6279 (pt0) cc_final: 0.5851 (tt0)
REVERT: D   51 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7525 (mt-10)
REVERT: D  120 LEU cc_start: 0.6472 (mt) cc_final: 0.6226 (mt)
REVERT: A   80 THR cc_start: 0.7379 (p) cc_final: 0.6813 (t)
REVERT: B   11 PHE cc_start: 0.5348 (OUTLIER) cc_final: 0.5131 (p90)
REVERT: B   67 MET cc_start: 0.7371 (tmm) cc_final: 0.6978 (ttt)
REVERT: J   98 ASN cc_start: 0.7824 (m-40) cc_final: 0.7604 (m-40)
REVERT: L   80 THR cc_start: 0.7303 (p) cc_final: 0.6713 (t)
REVERT: L  160 ASP cc_start: 0.6502 (t70) cc_final: 0.5916 (m-30)
REVERT: L  189 ARG cc_start: 0.4636 (ptt180) cc_final: 0.4310 (ptm-80)
REVERT: K   56 MET cc_start: 0.5424 (ppp) cc_final: 0.5219 (ppp)
  outliers start: 71
  outliers final: 55
  residues processed: 274
  average time/residue: 0.2747
  time to fit residues: 119.2466
Evaluate side-chains
  268 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 210
  time to evaluate  : 2.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   37 ASN
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue    9 SER
Chi-restraints excluded: chain B residue   11 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 LEU
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   19 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   12 THR
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 182 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 138 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 200 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 127 optimal weight:    0.3980
   chunk 98 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
C 179 ASN
J 179 ASN
** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.237999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.225227 restraints weight = 21895.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.205592 restraints weight = 32345.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.203887 restraints weight = 27665.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18888  Z= 0.129
  Angle     :  0.540   7.092  25428  Z= 0.293
  Chirality :  0.042   0.136   2832
  Planarity :  0.003   0.039   3252
  Dihedral  :  4.241  21.602   2520
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.81 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.18), residues: 2208
  helix:  1.08 (0.14), residues: 1488
  sheet: -2.29 (0.35), residues: 120
  loop : -2.50 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  62 
 HIS   0.009   0.001   HIS G  33 
 PHE   0.024   0.001   PHE D 180 
 TYR   0.027   0.001   TYR K  87 
 ARG   0.007   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04199 ( 1056)
  hydrogen bonds       : angle       3.98638 ( 3168)
  covalent geometry    : bond        0.00299 (18888)
  covalent geometry    : angle       0.54018 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 213
  time to evaluate  : 2.173 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4608 (OUTLIER) cc_final: 0.4127 (p90)
REVERT: E  105 GLU cc_start: 0.5425 (tt0) cc_final: 0.5124 (tt0)
REVERT: F    7 ASP cc_start: 0.6430 (t70) cc_final: 0.6197 (t0)
REVERT: C  151 GLU cc_start: 0.6277 (pt0) cc_final: 0.5822 (tt0)
REVERT: D   51 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7434 (mt-10)
REVERT: D  120 LEU cc_start: 0.6184 (mt) cc_final: 0.5934 (mt)
REVERT: A   20 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.4680 (m-80)
REVERT: A   70 LYS cc_start: 0.6794 (mmtm) cc_final: 0.6516 (mmtm)
REVERT: A   80 THR cc_start: 0.7371 (p) cc_final: 0.6749 (t)
REVERT: A  140 LYS cc_start: 0.7272 (ttmm) cc_final: 0.7002 (tmtt)
REVERT: B   67 MET cc_start: 0.7411 (tmm) cc_final: 0.7064 (ttt)
REVERT: J   98 ASN cc_start: 0.7791 (m-40) cc_final: 0.7575 (m-40)
REVERT: L   20 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.4500 (m-80)
REVERT: L   80 THR cc_start: 0.7261 (p) cc_final: 0.6685 (t)
REVERT: L  160 ASP cc_start: 0.6567 (t70) cc_final: 0.5914 (m-30)
REVERT: K   56 MET cc_start: 0.5182 (ppp) cc_final: 0.4891 (ppp)
  outliers start: 78
  outliers final: 53
  residues processed: 268
  average time/residue: 0.2851
  time to fit residues: 121.0723
Evaluate side-chains
  254 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 197
  time to evaluate  : 2.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   37 ASN
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue    8 THR
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue    9 SER
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue    8 THR
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  158 SER
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   50 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  108 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   19 THR
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain I residue   56 MET
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   12 THR
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 88 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 203 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9980
   chunk 196 optimal weight:    0.0040
   chunk 119 optimal weight:    0.0170
   chunk 75 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.3430

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

Flipped N/Q/H residues before XYZ refinement:
J 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.242948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.230230 restraints weight = 22029.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.211424 restraints weight = 31100.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.210224 restraints weight = 26151.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  18888  Z= 0.108
  Angle     :  0.526   9.068  25428  Z= 0.284
  Chirality :  0.041   0.148   2832
  Planarity :  0.003   0.043   3252
  Dihedral  :  4.030  22.250   2520
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.86 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.18), residues: 2208
  helix:  1.13 (0.14), residues: 1488
  sheet: -2.14 (0.35), residues: 120
  loop : -2.40 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP K  62 
 HIS   0.010   0.001   HIS F  33 
 PHE   0.028   0.001   PHE I 180 
 TYR   0.023   0.001   TYR K  87 
 ARG   0.007   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 ( 1056)
  hydrogen bonds       : angle       3.88665 ( 3168)
  covalent geometry    : bond        0.00229 (18888)
  covalent geometry    : angle       0.52631 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 221
  time to evaluate  : 2.284 
Fit side-chains
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.4197 (p90)
REVERT: E   67 MET cc_start: 0.7289 (tmm) cc_final: 0.6919 (tmm)
REVERT: F    7 ASP cc_start: 0.6216 (t70) cc_final: 0.5975 (t0)
REVERT: F   20 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.6113 (m-80)
REVERT: F  134 GLN cc_start: 0.7436 (tp-100) cc_final: 0.7148 (tt0)
REVERT: C  151 GLU cc_start: 0.6261 (pt0) cc_final: 0.5946 (tt0)
REVERT: D   51 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7346 (mt-10)
REVERT: D  120 LEU cc_start: 0.6301 (mt) cc_final: 0.6077 (mt)
REVERT: A   20 PHE cc_start: 0.5030 (OUTLIER) cc_final: 0.4667 (m-80)
REVERT: A   80 THR cc_start: 0.7401 (p) cc_final: 0.6744 (t)
REVERT: B   67 MET cc_start: 0.7306 (tmm) cc_final: 0.7038 (ttt)
REVERT: B  126 GLU cc_start: 0.4989 (mm-30) cc_final: 0.3655 (pt0)
REVERT: B  180 PHE cc_start: 0.2268 (t80) cc_final: 0.1687 (t80)
REVERT: J   67 MET cc_start: 0.4855 (OUTLIER) cc_final: 0.4503 (mtt)
REVERT: L   20 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.4460 (m-80)
REVERT: L   80 THR cc_start: 0.7217 (p) cc_final: 0.6666 (t)
REVERT: K   56 MET cc_start: 0.5190 (ppp) cc_final: 0.4834 (ppp)
  outliers start: 64
  outliers final: 39
  residues processed: 268
  average time/residue: 0.2989
  time to fit residues: 125.9019
Evaluate side-chains
  243 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 198
  time to evaluate  : 2.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   20 PHE
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  158 SER
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  108 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   12 THR
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue   67 MET
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 129 optimal weight:    6.9990
   chunk 101 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 149 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 175 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.234145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.219767 restraints weight = 22087.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.200846 restraints weight = 32599.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.198776 restraints weight = 34548.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  18888  Z= 0.185
  Angle     :  0.621   7.050  25428  Z= 0.333
  Chirality :  0.044   0.135   2832
  Planarity :  0.004   0.044   3252
  Dihedral  :  4.510  22.104   2520
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.36 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.18), residues: 2208
  helix:  1.00 (0.14), residues: 1488
  sheet: -2.35 (0.35), residues: 120
  loop : -2.44 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  62 
 HIS   0.009   0.001   HIS F  33 
 PHE   0.031   0.002   PHE D 180 
 TYR   0.026   0.002   TYR K  87 
 ARG   0.008   0.001   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 ( 1056)
  hydrogen bonds       : angle       4.13653 ( 3168)
  covalent geometry    : bond        0.00453 (18888)
  covalent geometry    : angle       0.62098 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 202
  time to evaluate  : 2.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4717 (OUTLIER) cc_final: 0.4035 (p90)
REVERT: F    7 ASP cc_start: 0.6528 (t70) cc_final: 0.6303 (t0)
REVERT: C  151 GLU cc_start: 0.6458 (pt0) cc_final: 0.5984 (tt0)
REVERT: D   51 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7294 (mt-10)
REVERT: D  120 LEU cc_start: 0.6623 (mt) cc_final: 0.6344 (mt)
REVERT: A   20 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4685 (m-80)
REVERT: A   80 THR cc_start: 0.7371 (p) cc_final: 0.6800 (t)
REVERT: B   67 MET cc_start: 0.7352 (tmm) cc_final: 0.7089 (ttt)
REVERT: H   33 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.6154 (p-80)
REVERT: J   67 MET cc_start: 0.4670 (OUTLIER) cc_final: 0.4348 (mtt)
REVERT: L   20 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.4502 (m-80)
REVERT: L   80 THR cc_start: 0.7320 (p) cc_final: 0.6756 (t)
REVERT: K   56 MET cc_start: 0.5397 (ppp) cc_final: 0.5065 (ppp)
  outliers start: 66
  outliers final: 49
  residues processed: 249
  average time/residue: 0.2752
  time to fit residues: 111.6125
Evaluate side-chains
  243 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 188
  time to evaluate  : 2.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  158 SER
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain C residue  181 LYS
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  178 LYS
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   33 HIS
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  158 SER
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue    8 THR
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  108 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue   20 PHE
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  103 ILE
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 204 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0770
   chunk 16 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   chunk 135 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.240200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.228398 restraints weight = 21993.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.225713 restraints weight = 29178.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.224271 restraints weight = 33776.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  18888  Z= 0.120
  Angle     :  0.554   7.745  25428  Z= 0.299
  Chirality :  0.042   0.134   2832
  Planarity :  0.004   0.042   3252
  Dihedral  :  4.214  22.596   2520
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.95 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.18), residues: 2208
  helix:  1.07 (0.14), residues: 1488
  sheet: -2.27 (0.34), residues: 120
  loop : -2.35 (0.21), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L  62 
 HIS   0.010   0.001   HIS G  33 
 PHE   0.032   0.001   PHE I 180 
 TYR   0.022   0.001   TYR K  87 
 ARG   0.007   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 ( 1056)
  hydrogen bonds       : angle       3.99999 ( 3168)
  covalent geometry    : bond        0.00265 (18888)
  covalent geometry    : angle       0.55358 (25428)

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

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

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4416 Ramachandran restraints generated.
    2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 195
  time to evaluate  : 2.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   11 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.4237 (p90)
REVERT: E   67 MET cc_start: 0.7190 (tmm) cc_final: 0.6839 (tmm)
REVERT: F    7 ASP cc_start: 0.6373 (t70) cc_final: 0.6124 (t0)
REVERT: C  151 GLU cc_start: 0.6329 (pt0) cc_final: 0.5857 (tt0)
REVERT: D   51 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7367 (mt-10)
REVERT: A    1 MET cc_start: 0.5956 (tpp) cc_final: 0.5725 (mmm)
REVERT: A   80 THR cc_start: 0.7590 (p) cc_final: 0.7152 (t)
REVERT: B  126 GLU cc_start: 0.5349 (mm-30) cc_final: 0.4568 (pt0)
REVERT: J   67 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.4022 (mtt)
REVERT: L   80 THR cc_start: 0.7464 (p) cc_final: 0.7076 (t)
REVERT: K   56 MET cc_start: 0.6030 (ppp) cc_final: 0.5793 (ppp)
  outliers start: 53
  outliers final: 42
  residues processed: 234
  average time/residue: 0.2627
  time to fit residues: 100.1954
Evaluate side-chains
  234 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 189
  time to evaluate  : 2.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 PHE
Chi-restraints excluded: chain E residue   12 THR
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   33 HIS
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   56 MET
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  183 ILE
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain F residue  106 GLU
Chi-restraints excluded: chain F residue  175 ILE
Chi-restraints excluded: chain F residue  183 ILE
Chi-restraints excluded: chain F residue  184 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  106 GLU
Chi-restraints excluded: chain D residue  175 ILE
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   84 ASP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain H residue   12 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain H residue  183 ILE
Chi-restraints excluded: chain G residue    8 THR
Chi-restraints excluded: chain G residue   32 ILE
Chi-restraints excluded: chain G residue  106 GLU
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 ILE
Chi-restraints excluded: chain G residue  184 LEU
Chi-restraints excluded: chain J residue   67 MET
Chi-restraints excluded: chain J residue  108 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue  106 GLU
Chi-restraints excluded: chain I residue  130 GLU
Chi-restraints excluded: chain I residue  175 ILE
Chi-restraints excluded: chain I residue  184 LEU
Chi-restraints excluded: chain L residue  132 LEU
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 202 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 141 optimal weight:    0.7980
   chunk 188 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 154 optimal weight:    8.9990
   chunk 84 optimal weight:    0.2980
   chunk 140 optimal weight:    1.9990
   chunk 126 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.240612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.227954 restraints weight = 22040.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.222524 restraints weight = 31149.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.220584 restraints weight = 46616.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  18888  Z= 0.118
  Angle     :  0.549   6.649  25428  Z= 0.297
  Chirality :  0.042   0.149   2832
  Planarity :  0.003   0.042   3252
  Dihedral  :  4.141  24.293   2520
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 23.40 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.18), residues: 2208
  helix:  1.09 (0.14), residues: 1488
  sheet: -2.28 (0.33), residues: 120
  loop : -2.32 (0.22), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP L  62 
 HIS   0.009   0.001   HIS G  33 
 PHE   0.016   0.001   PHE J  11 
 TYR   0.021   0.001   TYR K  87 
 ARG   0.007   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 ( 1056)
  hydrogen bonds       : angle       3.94971 ( 3168)
  covalent geometry    : bond        0.00262 (18888)
  covalent geometry    : angle       0.54864 (25428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5724.85 seconds
wall clock time: 100 minutes 6.14 seconds (6006.14 seconds total)