Starting phenix.real_space_refine
on Wed Aug  5 02:45:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/25il_80138/08_2026/25il_80138.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.103
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      53      5.16       5
     C    5301      2.51       5
     N    1390      2.21       5
     O    1523      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8267
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2492
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 82
    Chain: "C"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 397
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1939
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 230}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1700
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 6, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 82
    Chain: "S"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1739
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 36
  Time building chain proxies: 1.81, per 1000 atoms: 0.22
  Number of scatterers: 8267
  At special positions: 0
  Unit cell: (84.48, 119.04, 120.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1523      8.00
     N    1390      7.00
     C    5301      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 171 " - pdb=" SG  CYS R 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 469.9 milliseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      38.0% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.527A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 34 through 60
      Proline residue:  R  44  - end of helix
    Processing helix  chain 'R' and resid 66 through 92
    Processing helix  chain 'R' and resid 93 through 95
      No H-bonds generated for 'chain 'R' and resid 93 through 95'
    Processing helix  chain 'R' and resid 101 through 136
      removed outlier: 3.708A  pdb=" N   THR R 107 " --> pdb=" O   TYR R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 143
    Processing helix  chain 'R' and resid 147 through 171
      removed outlier: 3.668A  pdb=" N   MET R 170 " --> pdb=" O   MET R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 182 through 197
      removed outlier: 3.569A  pdb=" N   ALA R 186 " --> pdb=" O   ASN R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 198 through 216
      removed outlier: 3.574A  pdb=" N   LEU R 202 " --> pdb=" O   VAL R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 227 through 241
    Processing helix  chain 'R' and resid 241 through 254
      removed outlier: 4.570A  pdb=" N   ARG R 245 " --> pdb=" O   ALA R 241 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU R 249 " --> pdb=" O   ARG R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 281
      removed outlier: 3.701A  pdb=" N   HIS R 263 " --> pdb=" O   GLY R 259 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU R 266 " --> pdb=" O   HIS R 262 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU R 267 " --> pdb=" O   HIS R 263 " (cutoff:3.500A)
      Proline residue:  R 277  - end of helix
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.833A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 45
      removed outlier: 4.423A  pdb=" N   GLY A  45 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 42 through 45'
    Processing helix  chain 'A' and resid 94 through 99
      removed outlier: 3.551A  pdb=" N   ILE A  97 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLN A  98 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 133 through 137
      removed outlier: 4.448A  pdb=" N   THR A 136 " --> pdb=" O   TRP A 133 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 137 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 133 through 137'
    Processing helix  chain 'A' and resid 145 through 155
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.296A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 169
      removed outlier: 4.244A  pdb=" N   ALA A 168 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG A 169 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 164 through 169'
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.597A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
      removed outlier: 3.568A  pdb=" N   MET A 238 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.974A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.555A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.921A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.941A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.252A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.603A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.744A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.833A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 76
      removed outlier: 3.768A  pdb=" N   PHE A  74 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 9.449A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.507A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.092A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   CYS S  96 " --> pdb=" O   GLY S 112 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   GLY S 114 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 5.885A  pdb=" N   TYR S  94 " --> pdb=" O   GLY S 114 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 137
      removed outlier: 6.180A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1224 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 0.90 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: 2642
        1.34 -     1.46: 1771
        1.46 -     1.58: 3963
        1.58 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 8451
  Sorted by residual:
  bond pdb=" CA  ASN B 268 "
       pdb=" CB  ASN B 268 "
    ideal  model  delta    sigma   weight residual
    1.528  1.548 -0.020 1.66e-02 3.63e+03 1.46e+00
  bond pdb=" CB  ASN B 268 "
       pdb=" CG  ASN B 268 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" C   THR A 172 "
       pdb=" N   PRO A 173 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.012 1.27e-02 6.20e+03 9.10e-01
  bond pdb=" CB  ASP A 147 "
       pdb=" CG  ASP A 147 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.14e-01
  bond pdb=" C   VAL A 219 "
       pdb=" O   VAL A 219 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.19e-02 7.06e+03 7.63e-01
  ... (remaining 8446 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 11281
        1.44 -     2.88: 182
        2.88 -     4.32: 33
        4.32 -     5.76: 7
        5.76 -     7.20: 3
  Bond angle restraints: 11506
  Sorted by residual:
  angle pdb=" C   ALA R 241 "
        pdb=" N   MET R 242 "
        pdb=" CA  MET R 242 "
      ideal   model   delta    sigma   weight residual
     120.06  124.00   -3.94 1.19e+00 7.06e-01 1.10e+01
  angle pdb=" CA  ASN B 268 "
        pdb=" CB  ASN B 268 "
        pdb=" CG  ASN B 268 "
      ideal   model   delta    sigma   weight residual
     112.60  115.01   -2.41 1.00e+00 1.00e+00 5.80e+00
  angle pdb=" N   ASN R  64 "
        pdb=" CA  ASN R  64 "
        pdb=" C   ASN R  64 "
      ideal   model   delta    sigma   weight residual
     110.50  107.26    3.24 1.52e+00 4.33e-01 4.55e+00
  angle pdb=" C   ASN R  64 "
        pdb=" CA  ASN R  64 "
        pdb=" CB  ASN R  64 "
      ideal   model   delta    sigma   weight residual
     108.91  112.07   -3.16 1.53e+00 4.27e-01 4.25e+00
  angle pdb=" CA  LEU R  80 "
        pdb=" CB  LEU R  80 "
        pdb=" CG  LEU R  80 "
      ideal   model   delta    sigma   weight residual
     116.30  123.50   -7.20 3.50e+00 8.16e-02 4.23e+00
  ... (remaining 11501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 4250
       17.30 -    34.61: 514
       34.61 -    51.91: 152
       51.91 -    69.21: 13
       69.21 -    86.52: 12
  Dihedral angle restraints: 4941
    sinusoidal: 1772
      harmonic: 3169
  Sorted by residual:
  dihedral pdb=" CB  CYS R 171 "
           pdb=" SG  CYS R 171 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.52  -86.52     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.31  -42.31     1      1.00e+01 1.00e-02 2.50e+01
  dihedral pdb=" CB  CYS S  22 "
           pdb=" SG  CYS S  22 "
           pdb=" SG  CYS S  96 "
           pdb=" CB  CYS S  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.36   37.64     1      1.00e+01 1.00e-02 2.00e+01
  ... (remaining 4938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 837
       0.029 -    0.058: 312
       0.058 -    0.086: 106
       0.086 -    0.115: 70
       0.115 -    0.144: 13
  Chirality restraints: 1338
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  VAL S 187 "
            pdb=" N   VAL S 187 "
            pdb=" C   VAL S 187 "
            pdb=" CB  VAL S 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  ILE S 145 "
            pdb=" N   ILE S 145 "
            pdb=" C   ILE S 145 "
            pdb=" CB  ILE S 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 1335 not shown)

  Planarity restraints: 1447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.034 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO B  39 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET R 242 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO R 243 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO R 243 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 243 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.26e+00
        pdb=" C   THR B  87 "    0.031 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1444 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 336
        2.72 -     3.26: 8027
        3.26 -     3.81: 13507
        3.81 -     4.35: 17075
        4.35 -     4.90: 30131
  Nonbonded interactions: 69076
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O   THR R 270 "
            pdb=" OG  SER R 274 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.233 3.040
  ... (remaining 69071 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.950
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
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      :  0.002   0.036   8454  Z= 0.106
  Angle     :  0.508   7.202  11512  Z= 0.279
  Chirality :  0.040   0.144   1338
  Planarity :  0.003   0.052   1447
  Dihedral  : 16.438  80.399   2888
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 28.24 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.25), residues: 1069
  helix:  0.44 (0.26), residues: 355
  sheet:  0.17 (0.28), residues: 294
  loop : -0.49 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.011   0.001   TYR A 243 
 PHE   0.012   0.001   PHE S  68 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.11 ( 8451)
  covalent geometry    : angle       0.50754 /  0.28 (11506)
  SS BOND              : bond        0.00278 /  0.14 (    3)
  SS BOND              : angle       0.85508 /  0.43 (    6)
  hydrogen bonds       : bond        0.25405 / 17.91 (  429)
  hydrogen bonds       : angle       8.26874 /  5.76 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LYS cc_start: 0.7519 (mtpp) cc_final: 0.6837 (mptt)
REVERT: A  124 ASP cc_start: 0.8204 (t0) cc_final: 0.7925 (t0)
REVERT: A  241 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7885 (mtp180)
REVERT: S  103 TYR cc_start: 0.9131 (t80) cc_final: 0.8720 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0997
  time to fit residues: 16.2951
Evaluate side-chains
  115 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    0.0070
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.1602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 123 ASN
S 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.139795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.110685 restraints weight = 9501.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.53
r_work: 0.2934 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8454  Z= 0.134
  Angle     :  0.541   7.644  11512  Z= 0.292
  Chirality :  0.042   0.137   1338
  Planarity :  0.004   0.056   1447
  Dihedral  :  4.072  17.408   1174
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 24.27 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1069
  helix:  1.88 (0.27), residues: 354
  sheet:  0.25 (0.29), residues: 276
  loop : -0.34 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.020   0.001   TYR S 178 
 PHE   0.014   0.001   PHE R  66 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 8451)
  covalent geometry    : angle       0.54079 /  0.29 (11506)
  SS BOND              : bond        0.00536 /  0.27 (    3)
  SS BOND              : angle       0.90448 /  0.46 (    6)
  hydrogen bonds       : bond        0.05049 /  3.59 (  429)
  hydrogen bonds       : angle       5.01356 /  3.52 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  120 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8169 (mp)
REVERT: A   36 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8766 (mt)
REVERT: A   73 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7585 (mptt)
REVERT: A  113 SER cc_start: 0.8506 (t) cc_final: 0.8251 (p)
REVERT: A  124 ASP cc_start: 0.7987 (t0) cc_final: 0.7779 (t0)
REVERT: A  166 GLU cc_start: 0.7921 (tp30) cc_final: 0.7719 (tp30)
REVERT: A  194 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8069 (ttm-80)
  outliers start: 18
  outliers final: 9
  residues processed: 141
  average time/residue: 0.0928
  time to fit residues: 18.0461
Evaluate side-chains
  128 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  229 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  210 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 76 optimal weight:   40.0000
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 34 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 ASN
A 119 GLN
A 244 ASN
S 113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.135409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.107497 restraints weight = 9523.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.51
r_work: 0.2889 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8454  Z= 0.217
  Angle     :  0.586   9.938  11512  Z= 0.309
  Chirality :  0.044   0.138   1338
  Planarity :  0.004   0.055   1447
  Dihedral  :  4.251  18.512   1174
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.04 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1069
  helix:  2.04 (0.27), residues: 359
  sheet:  0.06 (0.29), residues: 282
  loop : -0.56 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S  38 
 TYR   0.020   0.001   TYR B  59 
 PHE   0.022   0.002   PHE R 114 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00519 /  0.22 ( 8451)
  covalent geometry    : angle       0.58599 /  0.31 (11506)
  SS BOND              : bond        0.00570 /  0.28 (    3)
  SS BOND              : angle       0.60324 /  0.30 (    6)
  hydrogen bonds       : bond        0.04935 /  3.50 (  429)
  hydrogen bonds       : angle       4.79269 /  3.37 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8523 (m-80) cc_final: 0.7546 (m-80)
REVERT: B   75 GLN cc_start: 0.8561 (mm110) cc_final: 0.8060 (mm-40)
REVERT: R  120 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8113 (mp)
REVERT: R  215 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6669 (tmm160)
REVERT: A   25 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7189 (mt-10)
REVERT: A   36 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8795 (mt)
REVERT: A   73 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8105 (mtpp)
REVERT: A  113 SER cc_start: 0.8521 (t) cc_final: 0.8244 (p)
REVERT: A  124 ASP cc_start: 0.8081 (t0) cc_final: 0.7698 (t0)
REVERT: A  194 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8092 (ttm-80)
  outliers start: 26
  outliers final: 20
  residues processed: 141
  average time/residue: 0.0933
  time to fit residues: 18.3256
Evaluate side-chains
  135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  215 ARG
Chi-restraints excluded: chain R residue  229 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0970
   chunk 89 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 ASN
S 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.140067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.111185 restraints weight = 9701.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.62
r_work: 0.2900 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8454  Z= 0.104
  Angle     :  0.485   7.659  11512  Z= 0.259
  Chirality :  0.041   0.137   1338
  Planarity :  0.003   0.055   1447
  Dihedral  :  3.912  18.369   1174
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.62 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.25), residues: 1069
  helix:  2.46 (0.27), residues: 359
  sheet:  0.13 (0.29), residues: 286
  loop : -0.47 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.015   0.001   TYR S 178 
 PHE   0.016   0.001   PHE R 114 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 8451)
  covalent geometry    : angle       0.48505 /  0.26 (11506)
  SS BOND              : bond        0.00492 /  0.24 (    3)
  SS BOND              : angle       0.55160 /  0.27 (    6)
  hydrogen bonds       : bond        0.03903 /  2.78 (  429)
  hydrogen bonds       : angle       4.45222 /  3.13 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8593 (m-80) cc_final: 0.7902 (m-80)
REVERT: R  120 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: A   25 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7414 (mt-10)
REVERT: A   36 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8808 (mt)
REVERT: A   82 HIS cc_start: 0.8661 (m170) cc_final: 0.8349 (m-70)
REVERT: A  124 ASP cc_start: 0.8230 (t0) cc_final: 0.7884 (t0)
REVERT: A  194 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8017 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7880 (mtp180)
REVERT: A  243 TYR cc_start: 0.8470 (m-80) cc_final: 0.8267 (m-80)
REVERT: S  128 MET cc_start: 0.8713 (mmm) cc_final: 0.8456 (mmm)
  outliers start: 23
  outliers final: 13
  residues processed: 133
  average time/residue: 0.1009
  time to fit residues: 18.4810
Evaluate side-chains
  124 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0070
   chunk 105 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0570
   chunk 98 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0370
   chunk 4 optimal weight:    0.2980
   chunk 71 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    0.2594

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.158005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.126251 restraints weight = 9338.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.70
r_work: 0.3163 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   8454  Z= 0.090
  Angle     :  0.472   6.431  11512  Z= 0.250
  Chirality :  0.040   0.193   1338
  Planarity :  0.003   0.054   1447
  Dihedral  :  3.650  17.348   1174
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 24.97 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.26), residues: 1069
  helix:  2.74 (0.26), residues: 359
  sheet:  0.21 (0.30), residues: 285
  loop : -0.35 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.014   0.001   PHE R 114 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00189 /  0.09 ( 8451)
  covalent geometry    : angle       0.47209 /  0.25 (11506)
  SS BOND              : bond        0.00286 /  0.14 (    3)
  SS BOND              : angle       0.88025 /  0.44 (    6)
  hydrogen bonds       : bond        0.03500 /  2.50 (  429)
  hydrogen bonds       : angle       4.23119 /  2.99 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8436 (m-80) cc_final: 0.7631 (m-80)
REVERT: B   75 GLN cc_start: 0.8509 (mm110) cc_final: 0.8245 (mm110)
REVERT: B  175 GLN cc_start: 0.8688 (mm110) cc_final: 0.8340 (mm110)
REVERT: B  323 ASP cc_start: 0.8842 (p0) cc_final: 0.8598 (p0)
REVERT: A   25 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7250 (mt-10)
REVERT: A   36 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8716 (mt)
REVERT: A   82 HIS cc_start: 0.8576 (m170) cc_final: 0.8348 (m-70)
REVERT: A  124 ASP cc_start: 0.7968 (t0) cc_final: 0.7603 (t0)
REVERT: A  166 GLU cc_start: 0.7950 (tp30) cc_final: 0.7218 (pt0)
REVERT: A  194 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7775 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7834 (mtp180)
REVERT: A  243 TYR cc_start: 0.8380 (m-80) cc_final: 0.8170 (m-80)
REVERT: S  128 MET cc_start: 0.8667 (mmm) cc_final: 0.8438 (mmm)
  outliers start: 21
  outliers final: 14
  residues processed: 133
  average time/residue: 0.0852
  time to fit residues: 16.0425
Evaluate side-chains
  125 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0010
   chunk 105 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:   50.0000
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3994

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.151220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.118584 restraints weight = 9342.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.71
r_work: 0.3073 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8454  Z= 0.130
  Angle     :  0.501   7.020  11512  Z= 0.264
  Chirality :  0.041   0.173   1338
  Planarity :  0.003   0.053   1447
  Dihedral  :  3.774  17.911   1174
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.27 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.26), residues: 1069
  helix:  2.75 (0.26), residues: 359
  sheet:  0.11 (0.30), residues: 287
  loop : -0.40 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.017   0.001   PHE R 114 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 8451)
  covalent geometry    : angle       0.50017 /  0.26 (11506)
  SS BOND              : bond        0.00386 /  0.19 (    3)
  SS BOND              : angle       1.04630 /  0.48 (    6)
  hydrogen bonds       : bond        0.03805 /  2.72 (  429)
  hydrogen bonds       : angle       4.27709 /  3.02 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8580 (m-80) cc_final: 0.7667 (m-80)
REVERT: B   75 GLN cc_start: 0.8688 (mm110) cc_final: 0.8449 (mm110)
REVERT: B  323 ASP cc_start: 0.8907 (p0) cc_final: 0.8657 (p0)
REVERT: R   61 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7678 (mtp)
REVERT: R  120 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8058 (mp)
REVERT: A   25 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7291 (mt-10)
REVERT: A   36 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8800 (mt)
REVERT: A   82 HIS cc_start: 0.8566 (m170) cc_final: 0.8353 (m-70)
REVERT: A  124 ASP cc_start: 0.8016 (t0) cc_final: 0.7626 (t0)
REVERT: A  151 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8014 (mt-10)
REVERT: A  166 GLU cc_start: 0.7971 (tp30) cc_final: 0.7231 (pt0)
REVERT: A  187 THR cc_start: 0.8631 (m) cc_final: 0.8378 (m)
REVERT: A  194 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7808 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7869 (mtp180)
REVERT: S   83 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8754 (mtp)
  outliers start: 27
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0893
  time to fit residues: 15.1269
Evaluate side-chains
  123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   61 MET
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0170
   chunk 66 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    2.1424

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.138567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.107943 restraints weight = 9591.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.68
r_work: 0.2896 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8454  Z= 0.172
  Angle     :  0.532   7.493  11512  Z= 0.281
  Chirality :  0.042   0.166   1338
  Planarity :  0.004   0.054   1447
  Dihedral  :  3.989  18.622   1174
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 23.45 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.25), residues: 1069
  helix:  2.65 (0.26), residues: 359
  sheet:  0.07 (0.30), residues: 284
  loop : -0.52 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.019   0.001   PHE R 114 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.17 ( 8451)
  covalent geometry    : angle       0.53156 /  0.28 (11506)
  SS BOND              : bond        0.00429 /  0.21 (    3)
  SS BOND              : angle       1.10704 /  0.50 (    6)
  hydrogen bonds       : bond        0.04086 /  2.91 (  429)
  hydrogen bonds       : angle       4.40760 /  3.10 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8481 (m-80) cc_final: 0.7556 (m-80)
REVERT: B   75 GLN cc_start: 0.8809 (mm110) cc_final: 0.8345 (mm-40)
REVERT: R   61 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7401 (mtp)
REVERT: R  120 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: R  215 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6498 (tmm160)
REVERT: A   25 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7109 (mt-10)
REVERT: A   36 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8734 (mt)
REVERT: A   82 HIS cc_start: 0.8456 (m170) cc_final: 0.8231 (m-70)
REVERT: A  124 ASP cc_start: 0.7854 (t0) cc_final: 0.7454 (t0)
REVERT: A  151 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: A  166 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7174 (pt0)
REVERT: A  187 THR cc_start: 0.8499 (m) cc_final: 0.8221 (m)
REVERT: A  194 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7808 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7813 (mtp180)
REVERT: S  128 MET cc_start: 0.8618 (mmm) cc_final: 0.8395 (mmm)
  outliers start: 34
  outliers final: 26
  residues processed: 127
  average time/residue: 0.0699
  time to fit residues: 12.5550
Evaluate side-chains
  132 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   61 MET
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  215 ARG
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.9982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.149548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.117723 restraints weight = 9400.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.70
r_work: 0.3056 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8454  Z= 0.110
  Angle     :  0.481   6.886  11512  Z= 0.255
  Chirality :  0.041   0.152   1338
  Planarity :  0.003   0.054   1447
  Dihedral  :  3.783  18.199   1174
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.04 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1069
  helix:  2.81 (0.26), residues: 359
  sheet:  0.11 (0.30), residues: 283
  loop : -0.49 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.017   0.001   PHE R 114 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 8451)
  covalent geometry    : angle       0.48059 /  0.25 (11506)
  SS BOND              : bond        0.00421 /  0.21 (    3)
  SS BOND              : angle       1.00834 /  0.46 (    6)
  hydrogen bonds       : bond        0.03639 /  2.59 (  429)
  hydrogen bonds       : angle       4.26551 /  3.01 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 ILE cc_start: 0.7786 (tt) cc_final: 0.7433 (mm)
REVERT: B   59 TYR cc_start: 0.8595 (m-80) cc_final: 0.7567 (m-80)
REVERT: R   61 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7472 (mtp)
REVERT: R  120 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8077 (mp)
REVERT: A   25 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7297 (mt-10)
REVERT: A   33 THR cc_start: 0.9264 (t) cc_final: 0.8869 (p)
REVERT: A   36 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8799 (mt)
REVERT: A   82 HIS cc_start: 0.8555 (m170) cc_final: 0.8310 (m-70)
REVERT: A  124 ASP cc_start: 0.8015 (t0) cc_final: 0.7641 (t0)
REVERT: A  151 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: A  166 GLU cc_start: 0.7997 (tp30) cc_final: 0.7320 (pt0)
REVERT: A  187 THR cc_start: 0.8657 (m) cc_final: 0.8397 (m)
REVERT: A  194 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7858 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7883 (mtp180)
REVERT: S   83 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8778 (mtp)
REVERT: S  128 MET cc_start: 0.8684 (mmm) cc_final: 0.8427 (mmm)
  outliers start: 27
  outliers final: 21
  residues processed: 121
  average time/residue: 0.0752
  time to fit residues: 13.0806
Evaluate side-chains
  123 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   61 MET
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 94 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.7382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.139434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.109080 restraints weight = 9538.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.68
r_work: 0.2962 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8454  Z= 0.149
  Angle     :  0.521   7.426  11512  Z= 0.274
  Chirality :  0.042   0.152   1338
  Planarity :  0.003   0.053   1447
  Dihedral  :  3.885  18.358   1174
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.80 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.25), residues: 1069
  helix:  2.74 (0.26), residues: 360
  sheet:  0.03 (0.30), residues: 286
  loop : -0.51 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.017   0.001   PHE R 114 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 ( 8451)
  covalent geometry    : angle       0.51717 /  0.27 (11506)
  SS BOND              : bond        0.00436 /  0.22 (    3)
  SS BOND              : angle       2.62782 /  1.38 (    6)
  hydrogen bonds       : bond        0.03897 /  2.76 (  429)
  hydrogen bonds       : angle       4.31496 /  3.04 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 ILE cc_start: 0.7765 (tt) cc_final: 0.7429 (mm)
REVERT: B   59 TYR cc_start: 0.8553 (m-80) cc_final: 0.7563 (m-80)
REVERT: R   61 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7469 (mtp)
REVERT: R  120 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: A   25 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7310 (mt-10)
REVERT: A   36 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8813 (mt)
REVERT: A  124 ASP cc_start: 0.7998 (t0) cc_final: 0.7628 (t0)
REVERT: A  151 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8067 (mt-10)
REVERT: A  166 GLU cc_start: 0.7952 (tp30) cc_final: 0.7328 (pt0)
REVERT: A  187 THR cc_start: 0.8673 (m) cc_final: 0.8401 (m)
REVERT: A  194 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7993 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7846 (mtp180)
REVERT: S   83 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (mtp)
  outliers start: 29
  outliers final: 23
  residues processed: 121
  average time/residue: 0.0734
  time to fit residues: 12.6245
Evaluate side-chains
  126 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   61 MET
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 102 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.152080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.121874 restraints weight = 9338.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.60
r_work: 0.3069 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8454  Z= 0.107
  Angle     :  0.484   7.248  11512  Z= 0.256
  Chirality :  0.041   0.147   1338
  Planarity :  0.003   0.054   1447
  Dihedral  :  3.762  18.007   1174
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.04 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1069
  helix:  2.88 (0.26), residues: 360
  sheet:  0.13 (0.30), residues: 283
  loop : -0.51 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.016   0.001   PHE R 114 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 8451)
  covalent geometry    : angle       0.48214 /  0.25 (11506)
  SS BOND              : bond        0.00478 /  0.24 (    3)
  SS BOND              : angle       2.01004 /  1.05 (    6)
  hydrogen bonds       : bond        0.03556 /  2.52 (  429)
  hydrogen bonds       : angle       4.23063 /  2.97 ( 1224)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 ILE cc_start: 0.7770 (tt) cc_final: 0.7407 (mm)
REVERT: B   59 TYR cc_start: 0.8573 (m-80) cc_final: 0.7675 (m-80)
REVERT: B   75 GLN cc_start: 0.8689 (mm110) cc_final: 0.8379 (mm110)
REVERT: B  323 ASP cc_start: 0.8904 (p0) cc_final: 0.8659 (p0)
REVERT: R   61 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7492 (mtp)
REVERT: R  120 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8070 (mp)
REVERT: R  170 MET cc_start: 0.7377 (ptp) cc_final: 0.7172 (mpp)
REVERT: A   25 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7355 (mt-10)
REVERT: A   33 THR cc_start: 0.9247 (t) cc_final: 0.8903 (p)
REVERT: A   36 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8834 (mt)
REVERT: A   73 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8144 (mtpp)
REVERT: A  124 ASP cc_start: 0.8088 (t0) cc_final: 0.7725 (t0)
REVERT: A  151 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8131 (mt-10)
REVERT: A  166 GLU cc_start: 0.8041 (tp30) cc_final: 0.7338 (pt0)
REVERT: A  187 THR cc_start: 0.8682 (m) cc_final: 0.8413 (m)
REVERT: A  194 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7898 (ttm-80)
REVERT: A  241 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7896 (mtp180)
REVERT: S   83 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8784 (mtp)
  outliers start: 25
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0715
  time to fit residues: 12.2168
Evaluate side-chains
  124 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   61 MET
Chi-restraints excluded: chain R residue   79 SER
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  220 ASP
Chi-restraints excluded: chain S residue   64 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:    0.0060
   chunk 26 optimal weight:    0.0010
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 41 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4004

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.145898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.114671 restraints weight = 9495.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.74
r_work: 0.3205 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   8454  Z= 0.088
  Angle     :  0.479   7.616  11512  Z= 0.251
  Chirality :  0.040   0.136   1338
  Planarity :  0.003   0.053   1447
  Dihedral  :  3.526  17.057   1174
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.97 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.26), residues: 1069
  helix:  3.06 (0.26), residues: 362
  sheet:  0.28 (0.30), residues: 284
  loop : -0.42 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  49 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.014   0.001   PHE R 114 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00194 /  0.09 ( 8451)
  covalent geometry    : angle       0.47764 /  0.25 (11506)
  SS BOND              : bond        0.00451 /  0.22 (    3)
  SS BOND              : angle       1.49170 /  0.77 (    6)
  hydrogen bonds       : bond        0.03226 /  2.29 (  429)
  hydrogen bonds       : angle       4.05312 /  2.86 ( 1224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2167.07 seconds
wall clock time: 37 minutes 44.06 seconds (2264.06 seconds total)