Starting phenix.real_space_refine
on Fri Nov 15 09:38:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ote_17176/11_2024/8ote_17176.cif"
  }
  resolution = 3.6
  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=   0.003
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      56      5.16       5
     C    5544      2.51       5
     N    1384      2.21       5
     O    1696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8680
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "E"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "F"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "G"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "H"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Time building chain proxies: 6.49, per 1000 atoms: 0.75
  Number of scatterers: 8680
  At special positions: 0
  Unit cell: (191.992, 144.2, 36.256, 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      56     16.00
     O    1696      8.00
     N    1384      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 214 " - pdb=" SG  CYS E 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 214 " - pdb=" SG  CYS F 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 214 " - pdb=" SG  CYS G 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 214 " - pdb=" SG  CYS H 253 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.05
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 23 sheets defined
      0.0% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 121 through 126
      removed outlier: 6.905A  pdb=" N   ASP A 122 " --> pdb=" O   ILE E 121 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE A 121 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   LYS C 124 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL A 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ILE C 126 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TYR A 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ILE C 121 " --> pdb=" O   ASP G 122 " (cutoff:3.500A)
      removed outlier: 9.042A  pdb=" N   LYS G 124 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL C 123 " --> pdb=" O   LYS G 124 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ILE G 126 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   TYR C 125 " --> pdb=" O   ILE G 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 129 through 130
      removed outlier: 6.680A  pdb=" N   LYS A 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS C 129 " --> pdb=" O   SER G 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 144 through 148
      removed outlier: 6.797A  pdb=" N   ILE E 146 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR A 147 " --> pdb=" O   ILE E 146 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN E 148 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   LEU A 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   THR C 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.434A  pdb=" N   ILE A 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   LEU C 144 " --> pdb=" O   ASN G 145 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   THR G 147 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 9.434A  pdb=" N   ILE C 146 " --> pdb=" O   THR G 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 155 through 157
      removed outlier: 6.668A  pdb=" N   ASN A 156 " --> pdb=" O   TYR E 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 163 through 165
      removed outlier: 6.409A  pdb=" N   GLU A 163 " --> pdb=" O   ASN E 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 168 through 175
      removed outlier: 6.894A  pdb=" N   VAL A 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   SER C 172 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   PHE A 171 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   THR C 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LYS A 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL C 169 " --> pdb=" O   GLN G 170 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   SER G 172 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   PHE C 171 " --> pdb=" O   SER G 172 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   THR G 174 " --> pdb=" O   PHE C 171 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LYS C 173 " --> pdb=" O   THR G 174 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 180 through 181
      removed outlier: 6.644A  pdb=" N   ARG A 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG C 180 " --> pdb=" O   LEU G 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 184 through 187
      removed outlier: 6.876A  pdb=" N   ILE A 184 " --> pdb=" O   SER E 185 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ILE E 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   ILE A 186 " --> pdb=" O   ILE E 187 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 201 through 206
      removed outlier: 6.795A  pdb=" N   THR A 201 " --> pdb=" O   VAL E 202 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ALA E 204 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE A 203 " --> pdb=" O   ALA E 204 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   GLU E 206 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU A 205 " --> pdb=" O   GLU E 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 230
      removed outlier: 6.165A  pdb=" N   VAL A 225 " --> pdb=" O   LEU E 226 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   MET E 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   MET A 227 " --> pdb=" O   MET E 228 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   VAL E 230 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   GLN A 229 " --> pdb=" O   VAL E 230 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL A 230 " --> pdb=" O   GLN C 229 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL C 230 " --> pdb=" O   GLN G 229 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 237
      removed outlier: 6.439A  pdb=" N   THR A 235 " --> pdb=" O   TYR E 236 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 246 through 247
      removed outlier: 6.278A  pdb=" N   GLU A 246 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   GLU C 246 " --> pdb=" O   ARG G 247 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 121 through 126
      removed outlier: 6.902A  pdb=" N   ASP B 122 " --> pdb=" O   ILE F 121 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE B 121 " --> pdb=" O   ASP D 122 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   LYS D 124 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL B 123 " --> pdb=" O   LYS D 124 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ILE D 126 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR B 125 " --> pdb=" O   ILE D 126 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE D 121 " --> pdb=" O   ASP H 122 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   LYS H 124 " --> pdb=" O   ILE D 121 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   VAL D 123 " --> pdb=" O   LYS H 124 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ILE H 126 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR D 125 " --> pdb=" O   ILE H 126 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 130
      removed outlier: 6.678A  pdb=" N   LYS B 129 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LYS D 129 " --> pdb=" O   SER H 130 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 148
      removed outlier: 6.128A  pdb=" N   THR B 147 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   THR D 147 " --> pdb=" O   ASN H 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 155 through 157
      removed outlier: 6.663A  pdb=" N   ASN B 156 " --> pdb=" O   TYR F 157 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 165
      removed outlier: 6.418A  pdb=" N   GLU B 163 " --> pdb=" O   ASN F 164 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 175
      removed outlier: 6.931A  pdb=" N   VAL B 169 " --> pdb=" O   GLN D 170 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   SER D 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   PHE B 171 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   THR D 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LYS B 173 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL D 169 " --> pdb=" O   GLN H 170 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   SER H 172 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   PHE D 171 " --> pdb=" O   SER H 172 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   THR H 174 " --> pdb=" O   PHE D 171 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   LYS D 173 " --> pdb=" O   THR H 174 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 180 through 181
      removed outlier: 6.650A  pdb=" N   ARG B 180 " --> pdb=" O   LEU D 181 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ARG D 180 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 184 through 187
      removed outlier: 6.903A  pdb=" N   ILE B 184 " --> pdb=" O   SER F 185 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   ILE F 187 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE B 186 " --> pdb=" O   ILE F 187 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 204
      removed outlier: 6.792A  pdb=" N   THR B 201 " --> pdb=" O   VAL F 202 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   ALA F 204 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ILE B 203 " --> pdb=" O   ALA F 204 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 224 through 230
      removed outlier: 6.161A  pdb=" N   VAL B 225 " --> pdb=" O   LEU F 226 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   MET F 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   MET B 227 " --> pdb=" O   MET F 228 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL F 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   GLN B 229 " --> pdb=" O   VAL F 230 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B 230 " --> pdb=" O   GLN D 229 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL D 230 " --> pdb=" O   GLN H 229 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 247
      removed outlier: 6.274A  pdb=" N   GLU B 246 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLU D 246 " --> pdb=" O   ARG H 247 " (cutoff:3.500A)

    98 hydrogen bonds defined for protein.
    294 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1852
        1.34 -     1.46: 2574
        1.46 -     1.58: 4302
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 8824
  Sorted by residual:
  bond pdb=" CA  SER A 130 "
       pdb=" CB  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 1.02e+01
  bond pdb=" CA  SER G 130 "
       pdb=" CB  SER G 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 1.01e+01
  bond pdb=" CA  SER E 130 "
       pdb=" CB  SER E 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.056 1.76e-02 3.23e+03 9.96e+00
  bond pdb=" CA  SER C 130 "
       pdb=" CB  SER C 130 "
    ideal  model  delta    sigma   weight residual
    1.534  1.478  0.055 1.76e-02 3.23e+03 9.89e+00
  bond pdb=" CA  SER H 130 "
       pdb=" CB  SER H 130 "
    ideal  model  delta    sigma   weight residual
    1.533  1.476  0.057 1.82e-02 3.02e+03 9.66e+00
  ... (remaining 8819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 8740
        1.61 -     3.22: 2385
        3.22 -     4.84: 686
        4.84 -     6.45: 165
        6.45 -     8.06: 16
  Bond angle restraints: 11992
  Sorted by residual:
  angle pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
        pdb=" C   GLU C 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.20   -8.06 1.52e+00 4.33e-01 2.81e+01
  angle pdb=" N   GLU G 246 "
        pdb=" CA  GLU G 246 "
        pdb=" C   GLU G 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.19   -8.05 1.52e+00 4.33e-01 2.81e+01
  angle pdb=" N   GLU A 246 "
        pdb=" CA  GLU A 246 "
        pdb=" C   GLU A 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.19   -8.05 1.52e+00 4.33e-01 2.80e+01
  angle pdb=" N   GLU E 246 "
        pdb=" CA  GLU E 246 "
        pdb=" C   GLU E 246 "
      ideal   model   delta    sigma   weight residual
     108.14  116.18   -8.04 1.52e+00 4.33e-01 2.80e+01
  angle pdb=" CA  ASP F 252 "
        pdb=" CB  ASP F 252 "
        pdb=" CG  ASP F 252 "
      ideal   model   delta    sigma   weight residual
     112.60  117.87   -5.27 1.00e+00 1.00e+00 2.78e+01
  ... (remaining 11987 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.48: 4285
       14.48 -    28.95: 683
       28.95 -    43.42: 196
       43.42 -    57.90: 116
       57.90 -    72.37: 40
  Dihedral angle restraints: 5320
    sinusoidal: 2072
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CA  ALA G 131 "
           pdb=" C   ALA G 131 "
           pdb=" N   TYR G 132 "
           pdb=" CA  TYR G 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.61   30.39     0      5.00e+00 4.00e-02 3.69e+01
  dihedral pdb=" CA  ALA H 131 "
           pdb=" C   ALA H 131 "
           pdb=" N   TYR H 132 "
           pdb=" CA  TYR H 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.65   30.35     0      5.00e+00 4.00e-02 3.68e+01
  dihedral pdb=" CA  ALA A 131 "
           pdb=" C   ALA A 131 "
           pdb=" N   TYR A 132 "
           pdb=" CA  TYR A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.65   30.35     0      5.00e+00 4.00e-02 3.68e+01
  ... (remaining 5317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 508
       0.056 -    0.112: 557
       0.112 -    0.169: 244
       0.169 -    0.225: 96
       0.225 -    0.281: 35
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  THR D 153 "
            pdb=" N   THR D 153 "
            pdb=" C   THR D 153 "
            pdb=" CB  THR D 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  THR B 153 "
            pdb=" N   THR B 153 "
            pdb=" C   THR B 153 "
            pdb=" CB  THR B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  THR H 153 "
            pdb=" N   THR H 153 "
            pdb=" C   THR H 153 "
            pdb=" CB  THR H 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 180 "    0.257 9.50e-02 1.11e+02   1.15e-01 9.10e+00
        pdb=" NE  ARG C 180 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 180 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 180 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 180 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 180 "   -0.256 9.50e-02 1.11e+02   1.15e-01 9.07e+00
        pdb=" NE  ARG D 180 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 180 "    0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 180 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 180 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 180 "    0.257 9.50e-02 1.11e+02   1.15e-01 9.06e+00
        pdb=" NE  ARG A 180 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 180 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 180 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 180 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2959
        2.88 -     3.39: 8779
        3.39 -     3.89: 14955
        3.89 -     4.40: 16737
        4.40 -     4.90: 32031
  Nonbonded interactions: 75461
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 138 "
            pdb=" OG1 THR A 141 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   GLN C 138 "
            pdb=" OG1 THR C 141 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   GLN E 138 "
            pdb=" OG1 THR E 141 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   GLN G 138 "
            pdb=" OG1 THR G 141 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" O   GLN H 138 "
            pdb=" OG1 THR H 141 "
     model   vdw
     2.378 3.040
  ... (remaining 75456 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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:             21.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.230
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
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      :  0.009   0.059   8824  Z= 0.581
  Angle     :  1.701   8.060  11992  Z= 1.088
  Chirality :  0.101   0.281   1440
  Planarity :  0.013   0.116   1488
  Dihedral  : 18.705  72.373   3216
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 10.32 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.77 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.76 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.51 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.005   HIS G 239 
 PHE   0.011   0.004   PHE C 237 
 TYR   0.046   0.008   TYR C 143 
 ARG   0.017   0.005   ARG D 180 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 171
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (ptmt)
REVERT: A  157 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.5896 (m-80)
REVERT: A  193 LYS cc_start: 0.8767 (tttt) cc_final: 0.8556 (ttmt)
REVERT: A  246 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8706 (pt0)
REVERT: B  157 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5883 (m-80)
REVERT: B  193 LYS cc_start: 0.8772 (tttt) cc_final: 0.8571 (ttmt)
REVERT: B  246 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8720 (pt0)
REVERT: C  129 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8190 (ptmt)
REVERT: C  138 GLN cc_start: 0.8378 (mt0) cc_final: 0.8070 (tt0)
REVERT: C  157 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5502 (m-80)
REVERT: C  246 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8627 (pt0)
REVERT: D  129 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8204 (ptmt)
REVERT: D  157 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5479 (m-80)
REVERT: D  246 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (pt0)
REVERT: E  129 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7939 (pttp)
REVERT: E  246 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (pt0)
REVERT: F  129 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7912 (pttp)
REVERT: F  246 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8443 (pt0)
REVERT: G  124 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8241 (mtpp)
REVERT: G  129 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8057 (ptmt)
REVERT: G  157 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6451 (m-80)
REVERT: G  210 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7750 (ttm)
REVERT: H  124 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8250 (mtpp)
REVERT: H  129 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7981 (ptmt)
REVERT: H  157 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6440 (m-80)
  outliers start: 64
  outliers final: 32
  residues processed: 211
  average time/residue: 0.2344
  time to fit residues: 65.7011
Evaluate side-chains
  195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 141
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  157 TYR
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  157 TYR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  157 TYR
Chi-restraints excluded: chain D residue  201 THR
Chi-restraints excluded: chain D residue  246 GLU
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  157 TYR
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  157 TYR
Chi-restraints excluded: chain F residue  201 THR
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  157 TYR
Chi-restraints excluded: chain G residue  201 THR
Chi-restraints excluded: chain G residue  210 MET
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  157 TYR
Chi-restraints excluded: chain H residue  201 THR
Chi-restraints excluded: chain H residue  246 GLU
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 78 optimal weight:    0.4980
   chunk 43 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 170 GLN
A 194 GLN
A 242 GLN
A 245 GLN
B 154 ASN
B 170 GLN
B 194 GLN
B 242 GLN
B 245 GLN
C 154 ASN
C 170 GLN
C 242 GLN
D 154 ASN
D 170 GLN
D 242 GLN
E 154 ASN
E 170 GLN
E 242 GLN
E 245 GLN
F 154 ASN
F 170 GLN
F 242 GLN
F 245 GLN
G 154 ASN
G 170 GLN
G 242 GLN
H 154 ASN
H 170 GLN
H 242 GLN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8824  Z= 0.199
  Angle     :  0.624   3.753  11992  Z= 0.358
  Chirality :  0.053   0.133   1440
  Planarity :  0.003   0.034   1488
  Dihedral  : 11.661  59.081   1317
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 10.71 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 222 
 PHE   0.014   0.003   PHE D 237 
 TYR   0.024   0.002   TYR D 236 
 ARG   0.002   0.001   ARG B 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 151
  time to evaluate  : 1.071 
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: A  129 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7560 (pttp)
REVERT: A  193 LYS cc_start: 0.8725 (tttt) cc_final: 0.8508 (ttmt)
REVERT: A  246 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7944 (pt0)
REVERT: B  193 LYS cc_start: 0.8767 (tttt) cc_final: 0.8533 (ttmt)
REVERT: B  206 GLU cc_start: 0.6053 (pt0) cc_final: 0.5440 (tm-30)
REVERT: B  246 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7956 (pt0)
REVERT: C  129 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7515 (pttp)
REVERT: D  129 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7439 (pttp)
REVERT: D  206 GLU cc_start: 0.6271 (pt0) cc_final: 0.5662 (tm-30)
REVERT: E  129 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7053 (pttp)
REVERT: E  153 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.7088 (p)
REVERT: E  182 ASN cc_start: 0.8906 (t0) cc_final: 0.8629 (t0)
REVERT: E  193 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8722 (mttt)
REVERT: E  206 GLU cc_start: 0.6496 (pt0) cc_final: 0.5677 (tm-30)
REVERT: E  246 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7894 (pt0)
REVERT: F  124 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7708 (mttm)
REVERT: F  129 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7072 (pttp)
REVERT: F  153 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7093 (p)
REVERT: F  182 ASN cc_start: 0.8897 (t0) cc_final: 0.8681 (t0)
REVERT: F  193 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8643 (mtpt)
REVERT: F  206 GLU cc_start: 0.6426 (pt0) cc_final: 0.5621 (tm-30)
REVERT: F  246 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7925 (pt0)
REVERT: G  129 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (ptmt)
REVERT: G  193 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8662 (mttt)
REVERT: H  129 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7643 (ptmt)
  outliers start: 56
  outliers final: 37
  residues processed: 196
  average time/residue: 0.2272
  time to fit residues: 60.5333
Evaluate side-chains
  190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 139
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  246 GLU
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  153 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  246 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
G 229 GLN
H 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8824  Z= 0.160
  Angle     :  0.563   4.629  11992  Z= 0.319
  Chirality :  0.051   0.129   1440
  Planarity :  0.003   0.030   1488
  Dihedral  : 10.076  59.356   1290
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 12.00 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 239 
 PHE   0.010   0.002   PHE A 213 
 TYR   0.025   0.002   TYR D 236 
 ARG   0.001   0.000   ARG G 140 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 140
  time to evaluate  : 1.047 
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: A  129 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7610 (pttp)
REVERT: A  193 LYS cc_start: 0.8682 (tttt) cc_final: 0.8468 (ttmt)
REVERT: A  206 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5450 (tm-30)
REVERT: A  246 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7730 (pt0)
REVERT: B  193 LYS cc_start: 0.8687 (tttt) cc_final: 0.8476 (ttmt)
REVERT: B  206 GLU cc_start: 0.6107 (pt0) cc_final: 0.5527 (tm-30)
REVERT: B  246 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7730 (pt0)
REVERT: C  206 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5471 (tm-30)
REVERT: D  206 GLU cc_start: 0.6205 (pt0) cc_final: 0.5560 (tm-30)
REVERT: E  193 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8711 (mtpt)
REVERT: E  246 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7609 (pt0)
REVERT: F  193 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8737 (mtpt)
REVERT: F  246 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7642 (pt0)
REVERT: G  193 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8606 (mttt)
REVERT: G  228 MET cc_start: 0.7705 (ttt) cc_final: 0.7486 (ttt)
REVERT: H  228 MET cc_start: 0.7740 (ttt) cc_final: 0.7527 (ttt)
REVERT: H  234 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8418 (m)
REVERT: H  236 TYR cc_start: 0.8649 (t80) cc_final: 0.8335 (t80)
  outliers start: 51
  outliers final: 36
  residues processed: 182
  average time/residue: 0.1931
  time to fit residues: 49.5717
Evaluate side-chains
  171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  246 GLU
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain D residue  124 LYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  246 GLU
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  246 GLU
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  246 GLU
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  246 GLU
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 71 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 63 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 194 GLN
B 156 ASN
B 194 GLN
C 156 ASN
D 156 ASN
E 156 ASN
F 156 ASN
G 156 ASN
H 156 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8824  Z= 0.426
  Angle     :  0.731   5.174  11992  Z= 0.417
  Chirality :  0.056   0.138   1440
  Planarity :  0.004   0.033   1488
  Dihedral  : 10.591  69.212   1263
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 17.26 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.20 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.14), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 222 
 PHE   0.013   0.003   PHE C 213 
 TYR   0.029   0.005   TYR G 157 
 ARG   0.002   0.000   ARG H 140 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 149
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7861 (mttm)
REVERT: A  129 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7442 (pttp)
REVERT: A  193 LYS cc_start: 0.8781 (tttt) cc_final: 0.8531 (ttmt)
REVERT: B  193 LYS cc_start: 0.8779 (tttt) cc_final: 0.8531 (ttmt)
REVERT: B  214 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8171 (t)
REVERT: C  124 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8095 (mttm)
REVERT: E  193 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8727 (mtpt)
REVERT: F  193 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8728 (mtpt)
REVERT: F  210 MET cc_start: 0.8705 (ttt) cc_final: 0.8386 (ttm)
REVERT: G  124 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7257 (mmmt)
REVERT: G  129 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7364 (ptmt)
REVERT: G  138 GLN cc_start: 0.8597 (mt0) cc_final: 0.8282 (tt0)
REVERT: G  192 MET cc_start: 0.8288 (mtt) cc_final: 0.8086 (ttm)
REVERT: G  193 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8788 (mtmt)
REVERT: G  228 MET cc_start: 0.8146 (ttt) cc_final: 0.7891 (ttt)
REVERT: H  228 MET cc_start: 0.8186 (ttt) cc_final: 0.7905 (ttt)
REVERT: H  236 TYR cc_start: 0.8890 (t80) cc_final: 0.8609 (t80)
  outliers start: 61
  outliers final: 45
  residues processed: 199
  average time/residue: 0.2026
  time to fit residues: 57.1544
Evaluate side-chains
  190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 139
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  245 GLN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  124 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  129 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 74 optimal weight:    0.1980
   chunk 41 optimal weight:    0.0870
   chunk 85 optimal weight:   20.0000
   chunk 69 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.6564

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
B 194 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8824  Z= 0.172
  Angle     :  0.586   4.997  11992  Z= 0.329
  Chirality :  0.052   0.137   1440
  Planarity :  0.002   0.023   1488
  Dihedral  :  7.286  49.831   1231
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.94 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.19), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F 239 
 PHE   0.010   0.002   PHE C 237 
 TYR   0.025   0.002   TYR C 236 
 ARG   0.001   0.000   ARG D 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 141
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7504 (pttp)
REVERT: A  193 LYS cc_start: 0.8733 (tttt) cc_final: 0.8495 (mttt)
REVERT: A  206 GLU cc_start: 0.6075 (pt0) cc_final: 0.5382 (tm-30)
REVERT: B  193 LYS cc_start: 0.8711 (tttt) cc_final: 0.8474 (mttt)
REVERT: B  206 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5464 (tm-30)
REVERT: C  234 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8372 (m)
REVERT: E  193 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8747 (mtpt)
REVERT: F  193 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8741 (mtpt)
REVERT: F  210 MET cc_start: 0.8663 (ttt) cc_final: 0.8358 (ttm)
REVERT: G  138 GLN cc_start: 0.8415 (mt0) cc_final: 0.8111 (tt0)
REVERT: G  193 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8701 (mtmt)
REVERT: G  227 MET cc_start: 0.8292 (mtm) cc_final: 0.8074 (mpp)
REVERT: G  228 MET cc_start: 0.7930 (ttt) cc_final: 0.7657 (ttt)
REVERT: H  227 MET cc_start: 0.8305 (mtm) cc_final: 0.8025 (mpp)
REVERT: H  228 MET cc_start: 0.7941 (ttt) cc_final: 0.7691 (ttt)
REVERT: H  234 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8398 (m)
REVERT: H  236 TYR cc_start: 0.8749 (t80) cc_final: 0.8546 (t80)
  outliers start: 52
  outliers final: 33
  residues processed: 184
  average time/residue: 0.1994
  time to fit residues: 51.6125
Evaluate side-chains
  171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 100 optimal weight:   20.0000
   chunk 83 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 245 GLN
** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8824  Z= 0.334
  Angle     :  0.685   5.163  11992  Z= 0.386
  Chirality :  0.055   0.140   1440
  Planarity :  0.003   0.023   1488
  Dihedral  :  7.508  46.577   1226
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 21.73 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 239 
 PHE   0.013   0.002   PHE C 237 
 TYR   0.027   0.004   TYR D 236 
 ARG   0.002   0.000   ARG F 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 146
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.8770 (tttt) cc_final: 0.8554 (ttmt)
REVERT: E  193 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8728 (mtpt)
REVERT: F  193 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8716 (mtpt)
REVERT: G  138 GLN cc_start: 0.8466 (mt0) cc_final: 0.8184 (tt0)
REVERT: G  192 MET cc_start: 0.8242 (mtt) cc_final: 0.8025 (ttm)
REVERT: G  193 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8748 (mtmt)
REVERT: G  228 MET cc_start: 0.8085 (ttt) cc_final: 0.7813 (ttt)
REVERT: H  129 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7303 (ptmt)
REVERT: H  228 MET cc_start: 0.8103 (ttt) cc_final: 0.7811 (ttt)
REVERT: H  236 TYR cc_start: 0.8869 (t80) cc_final: 0.8645 (t80)
  outliers start: 57
  outliers final: 52
  residues processed: 192
  average time/residue: 0.1852
  time to fit residues: 50.3445
Evaluate side-chains
  192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 139
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  193 LYS
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  210 MET
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  124 LYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   chunk 84 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
B 229 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.4400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8824  Z= 0.243
  Angle     :  0.632   6.004  11992  Z= 0.354
  Chirality :  0.053   0.139   1440
  Planarity :  0.003   0.020   1488
  Dihedral  :  6.940  39.660   1226
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 23.21 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 239 
 PHE   0.012   0.002   PHE C 237 
 TYR   0.024   0.003   TYR D 236 
 ARG   0.001   0.000   ARG E 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 138
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5458 (tm-30)
REVERT: C  234 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8386 (m)
REVERT: D  207 MET cc_start: 0.6207 (ttt) cc_final: 0.5691 (mtp)
REVERT: E  193 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8778 (mtpt)
REVERT: F  129 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7687 (pttp)
REVERT: F  210 MET cc_start: 0.8689 (ttt) cc_final: 0.8292 (ttm)
REVERT: G  138 GLN cc_start: 0.8384 (mt0) cc_final: 0.8107 (tt0)
REVERT: G  228 MET cc_start: 0.7980 (ttt) cc_final: 0.7708 (ttt)
REVERT: G  236 TYR cc_start: 0.8752 (t80) cc_final: 0.8505 (t80)
REVERT: H  124 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7183 (mmmt)
REVERT: H  129 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7593 (ptmt)
REVERT: H  228 MET cc_start: 0.8047 (ttt) cc_final: 0.7796 (ttt)
  outliers start: 56
  outliers final: 49
  residues processed: 185
  average time/residue: 0.1911
  time to fit residues: 49.5677
Evaluate side-chains
  190 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 136
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  210 MET
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  124 LYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    4.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.4480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8824  Z= 0.322
  Angle     :  0.685   6.693  11992  Z= 0.385
  Chirality :  0.054   0.139   1440
  Planarity :  0.003   0.021   1488
  Dihedral  :  7.236  39.812   1222
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 24.40 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 239 
 PHE   0.014   0.002   PHE C 237 
 TYR   0.037   0.004   TYR H 236 
 ARG   0.001   0.000   ARG E 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 141
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  207 MET cc_start: 0.6226 (ttt) cc_final: 0.5845 (mtp)
REVERT: E  129 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7270 (pttp)
REVERT: E  193 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8688 (mtpt)
REVERT: F  129 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7246 (pttp)
REVERT: F  193 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (mtpt)
REVERT: G  124 LYS cc_start: 0.8420 (ptpt) cc_final: 0.7276 (mmmt)
REVERT: G  138 GLN cc_start: 0.8445 (mt0) cc_final: 0.8162 (tt0)
REVERT: G  228 MET cc_start: 0.8089 (ttt) cc_final: 0.7807 (ttt)
REVERT: G  236 TYR cc_start: 0.8807 (t80) cc_final: 0.8574 (t80)
REVERT: H  129 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7591 (ptmt)
REVERT: H  228 MET cc_start: 0.8165 (ttt) cc_final: 0.7870 (ttt)
  outliers start: 58
  outliers final: 49
  residues processed: 189
  average time/residue: 0.1979
  time to fit residues: 52.2839
Evaluate side-chains
  194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 141
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  124 LYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  193 LYS
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  129 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  210 MET
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  193 LYS
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 84 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0470
   chunk 61 optimal weight:   30.0000
   chunk 98 optimal weight:    0.5980
   chunk 60 optimal weight:    6.9990
   overall best weight:    2.7284

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

Flipped N/Q/H residues before XYZ refinement:
G 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8824  Z= 0.224
  Angle     :  0.633   7.350  11992  Z= 0.352
  Chirality :  0.052   0.138   1440
  Planarity :  0.002   0.023   1488
  Dihedral  :  6.615  34.297   1218
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 25.60 %
    Favored  : 69.15 %
  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: -3.97 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 239 
 PHE   0.011   0.002   PHE C 237 
 TYR   0.033   0.003   TYR H 236 
 ARG   0.001   0.000   ARG F 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 134
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  234 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8364 (m)
REVERT: D  207 MET cc_start: 0.6190 (ttt) cc_final: 0.5737 (mtp)
REVERT: E  193 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8766 (mtpt)
REVERT: F  129 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7687 (pttp)
REVERT: F  210 MET cc_start: 0.8750 (ttt) cc_final: 0.8327 (ttm)
REVERT: G  124 LYS cc_start: 0.8177 (ptpt) cc_final: 0.6943 (mmmt)
REVERT: G  138 GLN cc_start: 0.8374 (mt0) cc_final: 0.8109 (tt0)
REVERT: G  228 MET cc_start: 0.8000 (ttt) cc_final: 0.7708 (ttt)
REVERT: G  236 TYR cc_start: 0.8737 (t80) cc_final: 0.8525 (t80)
REVERT: H  124 LYS cc_start: 0.8119 (ptpp) cc_final: 0.6538 (mmmt)
REVERT: H  129 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7560 (ptmt)
REVERT: H  228 MET cc_start: 0.8090 (ttt) cc_final: 0.7797 (ttt)
  outliers start: 53
  outliers final: 45
  residues processed: 182
  average time/residue: 0.1928
  time to fit residues: 49.0874
Evaluate side-chains
  182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 134
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LYS
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  206 GLU
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  210 MET
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain E residue  253 CYS
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  129 LYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Chi-restraints excluded: chain H residue  253 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
G 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8824  Z= 0.203
  Angle     :  0.617   6.999  11992  Z= 0.342
  Chirality :  0.052   0.140   1440
  Planarity :  0.002   0.019   1488
  Dihedral  :  6.259  34.030   1214
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 25.79 %
    Favored  : 69.64 %
  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: -3.88 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 239 
 PHE   0.011   0.001   PHE C 237 
 TYR   0.032   0.002   TYR H 236 
 ARG   0.001   0.000   ARG F 247 

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 138
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 LYS cc_start: 0.9022 (mttp) cc_final: 0.8683 (mtpt)
REVERT: D  207 MET cc_start: 0.6243 (ttt) cc_final: 0.5749 (mtp)
REVERT: E  193 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8709 (mtpt)
REVERT: F  129 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (pttp)
REVERT: F  182 ASN cc_start: 0.8913 (t0) cc_final: 0.8669 (t0)
REVERT: G  138 GLN cc_start: 0.8335 (mt0) cc_final: 0.8081 (tt0)
REVERT: G  228 MET cc_start: 0.7880 (ttt) cc_final: 0.7644 (ttt)
REVERT: G  236 TYR cc_start: 0.8746 (t80) cc_final: 0.8523 (t80)
REVERT: H  124 LYS cc_start: 0.8142 (ptpp) cc_final: 0.6559 (mmmt)
REVERT: H  228 MET cc_start: 0.7997 (ttt) cc_final: 0.7704 (ttt)
  outliers start: 46
  outliers final: 41
  residues processed: 180
  average time/residue: 0.1902
  time to fit residues: 48.3199
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  137 VAL
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  206 GLU
Chi-restraints excluded: chain D residue  214 CYS
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain E residue  124 LYS
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  234 THR
Chi-restraints excluded: chain F residue  129 LYS
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  253 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  149 THR
Chi-restraints excluded: chain G residue  206 GLU
Chi-restraints excluded: chain G residue  214 CYS
Chi-restraints excluded: chain G residue  231 THR
Chi-restraints excluded: chain G residue  253 CYS
Chi-restraints excluded: chain H residue  137 VAL
Chi-restraints excluded: chain H residue  149 THR
Chi-restraints excluded: chain H residue  206 GLU
Chi-restraints excluded: chain H residue  214 CYS
Chi-restraints excluded: chain H residue  231 THR
Chi-restraints excluded: chain H residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
F 194 GLN
G 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.123785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.109973 restraints weight = 15474.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.112280 restraints weight = 6914.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.113904 restraints weight = 4092.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8824  Z= 0.332
  Angle     :  0.704   7.146  11992  Z= 0.392
  Chirality :  0.054   0.152   1440
  Planarity :  0.003   0.024   1488
  Dihedral  :  6.755  33.656   1209
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 25.40 %
    Favored  : 69.74 %
  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: -3.99 (0.20), residues: 1064
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.15), residues: 1064

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 239 
 PHE   0.014   0.002   PHE C 237 
 TYR   0.034   0.004   TYR H 236 
 ARG   0.001   0.000   ARG H 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2116.32 seconds
wall clock time: 49 minutes 57.18 seconds (2997.18 seconds total)