Starting phenix.real_space_refine
on Sun Jun 15 10:03:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xta_33444/06_2025/7xta_33444_neut_trim.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    5607      2.51       5
     N    1476      2.21       5
     O    1618      1.98       5
     H    8707      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17478
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 3538
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5026
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "E"
      Number of atoms: 3472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3472
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 794
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "R"
      Number of atoms: 4635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 4635
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.60, per 1000 atoms: 0.43
  Number of scatterers: 17478
  At special positions: 0
  Unit cell: (115.668, 128.52, 110.313, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     O    1618      8.00
     N    1476      7.00
     C    5607      6.00
     H    8707      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.03
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2088

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 12 sheets defined
      40.0% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.649A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.068A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 232'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.861A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.205A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 281
      No H-bonds generated for 'chain 'A' and resid 280 through 281'
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.868A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 9 through 25
      removed outlier: 4.063A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.641A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.570A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 19 through 46
    Processing helix  chain 'R' and resid 46 through 51
    Processing helix  chain 'R' and resid 53 through 72
      removed outlier: 4.329A  pdb=" N   PHE R  57 " --> pdb=" O   LYS R  53 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE R  58 " --> pdb=" O   THR R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 83
      removed outlier: 3.664A  pdb=" N   VAL R  81 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 123
      removed outlier: 4.297A  pdb=" N   PHE R  91 " --> pdb=" O   TYR R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 132
    Processing helix  chain 'R' and resid 133 through 153
      removed outlier: 3.542A  pdb=" N   ILE R 137 " --> pdb=" O   THR R 133 " (cutoff:3.500A)
      Proline residue:  R 148  - end of helix
      removed outlier: 3.912A  pdb=" N   ILE R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 153 through 158
      removed outlier: 3.654A  pdb=" N   GLN R 158 " --> pdb=" O   LEU R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 174
      removed outlier: 3.848A  pdb=" N   PHE R 174 " --> pdb=" O   GLU R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 200
    Processing helix  chain 'R' and resid 200 through 222
    Processing helix  chain 'R' and resid 255 through 281
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 282 through 284
      No H-bonds generated for 'chain 'R' and resid 282 through 284'
    Processing helix  chain 'R' and resid 289 through 312
      removed outlier: 3.770A  pdb=" N   ASN R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER R 304 " --> pdb=" O   GLY R 300 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY R 305 " --> pdb=" O   TYR R 301 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 317 through 328
      removed outlier: 3.942A  pdb=" N   ALA R 321 " --> pdb=" O   SER R 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.880A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.903A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.726A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.656A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.964A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.969A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.511A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.594A  pdb=" N   VAL E   5 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 7.156A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.128A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1194 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: 6.27

  Time building geometry restraints manager: 4.92 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8668
        1.03 -     1.23: 40
        1.23 -     1.42: 3793
        1.42 -     1.62: 5066
        1.62 -     1.81: 99
  Bond restraints: 17666
  Sorted by residual:
  bond pdb=" CZ2 SRO R 401 "
       pdb=" CH2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.521 -0.135 2.00e-02 2.50e+03 4.59e+01
  bond pdb=" CG  SRO R 401 "
       pdb=" CD2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.438  1.508 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" CD1 SRO R 401 "
       pdb=" NE1 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.377  1.315  0.062 2.00e-02 2.50e+03 9.71e+00
  bond pdb=" CE2 SRO R 401 "
       pdb=" CZ2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.352  0.041 2.00e-02 2.50e+03 4.17e+00
  bond pdb=" CD2 SRO R 401 "
       pdb=" CE3 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.404  1.366  0.038 2.00e-02 2.50e+03 3.66e+00
  ... (remaining 17661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 31668
        2.09 -     4.17: 120
        4.17 -     6.26: 16
        6.26 -     8.34: 2
        8.34 -    10.43: 1
  Bond angle restraints: 31807
  Sorted by residual:
  angle pdb=" CD1 SRO R 401 "
        pdb=" NE1 SRO R 401 "
        pdb=" CE2 SRO R 401 "
      ideal   model   delta    sigma   weight residual
     109.10  119.53  -10.43 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" CG  SRO R 401 "
        pdb=" CD1 SRO R 401 "
        pdb=" NE1 SRO R 401 "
      ideal   model   delta    sigma   weight residual
     110.16  102.15    8.01 3.00e+00 1.11e-01 7.12e+00
  angle pdb=" CB  LYS R 171 "
        pdb=" CG  LYS R 171 "
        pdb=" CD  LYS R 171 "
      ideal   model   delta    sigma   weight residual
     111.30  116.87   -5.57 2.30e+00 1.89e-01 5.86e+00
  angle pdb=" C   LEU R  80 "
        pdb=" N   VAL R  81 "
        pdb=" CA  VAL R  81 "
      ideal   model   delta    sigma   weight residual
     123.16  120.63    2.53 1.06e+00 8.90e-01 5.71e+00
  angle pdb=" CA  HIS R 223 "
        pdb=" C   HIS R 223 "
        pdb=" N   GLN R 224 "
      ideal   model   delta    sigma   weight residual
     117.21  120.56   -3.35 1.42e+00 4.96e-01 5.56e+00
  ... (remaining 31802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 7598
       17.10 -    34.21: 542
       34.21 -    51.31: 142
       51.31 -    68.42: 45
       68.42 -    85.52: 9
  Dihedral angle restraints: 8336
    sinusoidal: 4444
      harmonic: 3892
  Sorted by residual:
  dihedral pdb=" CA  HIS R 221 "
           pdb=" C   HIS R 221 "
           pdb=" N   ALA R 222 "
           pdb=" CA  ALA R 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  ... (remaining 8333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 995
       0.034 -    0.069: 256
       0.069 -    0.103: 75
       0.103 -    0.138: 49
       0.138 -    0.172: 2
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" CA  MET R  73 "
            pdb=" N   MET R  73 "
            pdb=" C   MET R  73 "
            pdb=" CB  MET R  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.41e-01
  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    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  VAL R 288 "
            pdb=" N   VAL R 288 "
            pdb=" C   VAL R 288 "
            pdb=" CB  VAL R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1374 not shown)

  Planarity restraints: 2597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.062 5.00e-02 4.00e+02   9.28e-02 1.38e+01
        pdb=" N   PRO B 236 "    0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.66e+00
        pdb=" N   PRO B  39 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 119 "   -0.013 2.00e-02 2.50e+03   9.48e-03 2.70e+00
        pdb=" CG  TYR R 119 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 119 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 119 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 119 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 119 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR R 119 "    0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR R 119 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR R 119 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR R 119 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2594 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 808
        2.18 -     2.78: 34729
        2.78 -     3.39: 48052
        3.39 -     3.99: 61642
        3.99 -     4.60: 96141
  Nonbonded interactions: 241372
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" HE  ARG B 314 "
     model   vdw
     1.573 2.450
  nonbonded pdb="HE21 GLN B 220 "
            pdb=" OD2 ASP B 258 "
     model   vdw
     1.576 2.450
  nonbonded pdb=" O   ALA A  41 "
            pdb=" HZ2 LYS A  46 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" H   GLN B 156 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" HH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     1.637 2.450
  ... (remaining 241367 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:             0.470
  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:             0.270
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     37.230
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.135   8959  Z= 0.158
  Angle     :  0.539  10.426  12135  Z= 0.307
  Chirality :  0.039   0.172   1377
  Planarity :  0.004   0.093   1523
  Dihedral  : 12.648  79.887   3207
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1097
  helix:  2.24 (0.28), residues: 381
  sheet:  1.15 (0.31), residues: 271
  loop :  0.09 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 332 
 HIS   0.001   0.000   HIS E  35 
 PHE   0.023   0.001   PHE B 235 
 TYR   0.027   0.001   TYR R 119 
 ARG   0.008   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18603 (  426)
  hydrogen bonds       : angle       6.68593 ( 1194)
  covalent geometry    : bond        0.00303 ( 8959)
  covalent geometry    : angle       0.53934 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  354 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 354
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7476 (ttm-80)
REVERT: A  275 GLU cc_start: 0.7477 (tp30) cc_final: 0.7232 (tp30)
REVERT: A  309 ASP cc_start: 0.7354 (m-30) cc_final: 0.6902 (m-30)
REVERT: B  111 TYR cc_start: 0.8528 (m-80) cc_final: 0.7499 (m-80)
REVERT: B  134 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.6976 (ptp-170)
REVERT: B  149 CYS cc_start: 0.7454 (m) cc_final: 0.7227 (m)
REVERT: B  170 ASP cc_start: 0.8135 (t70) cc_final: 0.7713 (t0)
REVERT: B  256 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8153 (mtm180)
REVERT: B  298 ASP cc_start: 0.7563 (t70) cc_final: 0.7249 (t0)
REVERT: B  317 CYS cc_start: 0.7113 (p) cc_final: 0.6908 (p)
REVERT: B  321 THR cc_start: 0.7243 (p) cc_final: 0.6959 (p)
REVERT: B  323 ASP cc_start: 0.7115 (p0) cc_final: 0.6763 (p0)
REVERT: E   67 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6857 (ttm170)
REVERT: G   14 LYS cc_start: 0.8030 (pttm) cc_final: 0.7818 (pttm)
REVERT: G   58 GLU cc_start: 0.7418 (mp0) cc_final: 0.7105 (mp0)
REVERT: R   53 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6636 (mmtp)
REVERT: R   79 GLU cc_start: 0.7659 (tt0) cc_final: 0.7448 (tt0)
REVERT: R  112 CYS cc_start: 0.7292 (m) cc_final: 0.6707 (m)
REVERT: R  139 LEU cc_start: 0.7271 (tp) cc_final: 0.6972 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 354
  average time/residue: 0.5484
  time to fit residues: 254.0521
Evaluate side-chains
  319 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
R 221 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.131532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.112854 restraints weight = 37479.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.44
r_work: 0.3370 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8959  Z= 0.251
  Angle     :  0.568   5.455  12135  Z= 0.314
  Chirality :  0.042   0.155   1377
  Planarity :  0.004   0.046   1523
  Dihedral  :  4.317  20.351   1207
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.68 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1097
  helix:  2.01 (0.27), residues: 383
  sheet:  0.83 (0.30), residues: 286
  loop : -0.16 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 109 
 PHE   0.018   0.002   PHE B 234 
 TYR   0.016   0.002   TYR E  60 
 ARG   0.007   0.001   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04940 (  426)
  hydrogen bonds       : angle       5.06985 ( 1194)
  covalent geometry    : bond        0.00532 ( 8959)
  covalent geometry    : angle       0.56824 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 334
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8128 (m-30) cc_final: 0.7867 (m-30)
REVERT: A   21 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7931 (ttm-80)
REVERT: A  204 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8078 (mm-40)
REVERT: A  205 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7833 (mmt-90)
REVERT: A  252 SER cc_start: 0.8603 (t) cc_final: 0.8273 (p)
REVERT: A  275 GLU cc_start: 0.7985 (tp30) cc_final: 0.7534 (tp30)
REVERT: A  309 ASP cc_start: 0.7752 (m-30) cc_final: 0.7344 (m-30)
REVERT: B   13 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: B   87 THR cc_start: 0.8632 (m) cc_final: 0.8350 (p)
REVERT: B  111 TYR cc_start: 0.8839 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  134 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7823 (ptp-170)
REVERT: B  149 CYS cc_start: 0.8358 (m) cc_final: 0.8128 (m)
REVERT: B  189 SER cc_start: 0.8844 (p) cc_final: 0.8581 (t)
REVERT: B  220 GLN cc_start: 0.8026 (mt0) cc_final: 0.7511 (mt0)
REVERT: B  256 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8351 (mtm180)
REVERT: B  258 ASP cc_start: 0.8037 (t0) cc_final: 0.7642 (t0)
REVERT: B  321 THR cc_start: 0.7595 (p) cc_final: 0.7351 (p)
REVERT: E   68 PHE cc_start: 0.7930 (m-10) cc_final: 0.7708 (m-10)
REVERT: G   14 LYS cc_start: 0.8299 (pttm) cc_final: 0.7915 (pttm)
REVERT: R   53 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6795 (mmtp)
REVERT: R   72 VAL cc_start: 0.8252 (t) cc_final: 0.7908 (t)
REVERT: R   90 VAL cc_start: 0.8308 (t) cc_final: 0.8103 (p)
REVERT: R  112 CYS cc_start: 0.8116 (m) cc_final: 0.7696 (m)
REVERT: R  139 LEU cc_start: 0.7239 (tp) cc_final: 0.6976 (tp)
REVERT: R  185 PHE cc_start: 0.8344 (t80) cc_final: 0.7995 (t80)
REVERT: R  301 TYR cc_start: 0.8206 (m-10) cc_final: 0.7561 (m-10)
  outliers start: 10
  outliers final: 8
  residues processed: 337
  average time/residue: 0.5830
  time to fit residues: 253.6288
Evaluate side-chains
  331 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 323
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue  183 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 85 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
E  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.132418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.113633 restraints weight = 37470.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.47
r_work: 0.3366 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8959  Z= 0.174
  Angle     :  0.511   5.441  12135  Z= 0.279
  Chirality :  0.040   0.140   1377
  Planarity :  0.004   0.066   1523
  Dihedral  :  4.230  20.099   1207
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.86 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1097
  helix:  1.95 (0.27), residues: 384
  sheet:  0.50 (0.29), residues: 286
  loop : -0.26 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 109 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.006   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  426)
  hydrogen bonds       : angle       4.81863 ( 1194)
  covalent geometry    : bond        0.00369 ( 8959)
  covalent geometry    : angle       0.51069 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 331
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8092 (m-30) cc_final: 0.7844 (m-30)
REVERT: A   21 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7892 (ttm-80)
REVERT: A  190 THR cc_start: 0.8975 (m) cc_final: 0.8748 (p)
REVERT: A  204 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8125 (mm-40)
REVERT: A  252 SER cc_start: 0.8597 (t) cc_final: 0.8276 (p)
REVERT: A  275 GLU cc_start: 0.8039 (tp30) cc_final: 0.7578 (tp30)
REVERT: A  309 ASP cc_start: 0.7721 (m-30) cc_final: 0.7299 (m-30)
REVERT: B   13 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: B   44 GLN cc_start: 0.7592 (pm20) cc_final: 0.7352 (pm20)
REVERT: B   76 ASP cc_start: 0.7611 (m-30) cc_final: 0.7300 (m-30)
REVERT: B  111 TYR cc_start: 0.8838 (m-80) cc_final: 0.8495 (m-80)
REVERT: B  134 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7820 (ptp-170)
REVERT: B  189 SER cc_start: 0.8861 (p) cc_final: 0.8581 (t)
REVERT: B  220 GLN cc_start: 0.8037 (mt0) cc_final: 0.7835 (mt0)
REVERT: B  256 ARG cc_start: 0.8674 (mtp85) cc_final: 0.8353 (mtm180)
REVERT: B  321 THR cc_start: 0.7549 (p) cc_final: 0.7265 (p)
REVERT: B  323 ASP cc_start: 0.7731 (p0) cc_final: 0.7463 (p0)
REVERT: E  234 GLU cc_start: 0.7999 (pt0) cc_final: 0.7688 (pp20)
REVERT: G   14 LYS cc_start: 0.8299 (pttm) cc_final: 0.7954 (pttm)
REVERT: G   58 GLU cc_start: 0.8026 (mp0) cc_final: 0.7625 (mp0)
REVERT: R   53 LYS cc_start: 0.7071 (mmtp) cc_final: 0.6818 (mmtp)
REVERT: R   72 VAL cc_start: 0.8260 (t) cc_final: 0.7833 (t)
REVERT: R   90 VAL cc_start: 0.8299 (t) cc_final: 0.8073 (p)
REVERT: R  112 CYS cc_start: 0.8214 (m) cc_final: 0.7747 (m)
REVERT: R  139 LEU cc_start: 0.7218 (tp) cc_final: 0.6933 (tp)
REVERT: R  185 PHE cc_start: 0.8369 (t80) cc_final: 0.8018 (t80)
REVERT: R  301 TYR cc_start: 0.8034 (m-10) cc_final: 0.7376 (m-10)
REVERT: R  306 LEU cc_start: 0.7903 (mt) cc_final: 0.7399 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 333
  average time/residue: 0.5604
  time to fit residues: 242.6292
Evaluate side-chains
  330 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 318
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
R  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.129346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110829 restraints weight = 37552.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.44
r_work: 0.3320 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   8959  Z= 0.293
  Angle     :  0.567   4.733  12135  Z= 0.316
  Chirality :  0.042   0.151   1377
  Planarity :  0.004   0.058   1523
  Dihedral  :  4.514  20.942   1207
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.70 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1097
  helix:  1.80 (0.27), residues: 382
  sheet:  0.05 (0.29), residues: 296
  loop : -0.42 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 176 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.016   0.002   PHE E  68 
 TYR   0.015   0.002   TYR E 190 
 ARG   0.006   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04804 (  426)
  hydrogen bonds       : angle       4.89489 ( 1194)
  covalent geometry    : bond        0.00623 ( 8959)
  covalent geometry    : angle       0.56673 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  355 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 330
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8093 (m-30) cc_final: 0.7860 (m-30)
REVERT: A   21 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7930 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7907 (tt0) cc_final: 0.7648 (tt0)
REVERT: A   28 GLU cc_start: 0.8108 (tt0) cc_final: 0.7896 (tt0)
REVERT: A   46 LYS cc_start: 0.8388 (mtmm) cc_final: 0.7753 (mtmt)
REVERT: A  204 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8181 (mm-40)
REVERT: A  252 SER cc_start: 0.8676 (t) cc_final: 0.8314 (p)
REVERT: A  275 GLU cc_start: 0.8022 (tp30) cc_final: 0.7605 (tp30)
REVERT: B   13 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: B   44 GLN cc_start: 0.7628 (pm20) cc_final: 0.7385 (pm20)
REVERT: B   76 ASP cc_start: 0.7778 (m-30) cc_final: 0.7406 (m-30)
REVERT: B  110 ASN cc_start: 0.8580 (m-40) cc_final: 0.8351 (m110)
REVERT: B  134 ARG cc_start: 0.8197 (ptp-170) cc_final: 0.7909 (ptp-170)
REVERT: B  172 GLU cc_start: 0.8635 (tp30) cc_final: 0.8401 (tp30)
REVERT: B  189 SER cc_start: 0.8869 (p) cc_final: 0.8609 (t)
REVERT: B  256 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8371 (mtm180)
REVERT: B  321 THR cc_start: 0.7526 (p) cc_final: 0.7237 (p)
REVERT: B  323 ASP cc_start: 0.7751 (p0) cc_final: 0.7472 (p0)
REVERT: E  220 GLU cc_start: 0.7318 (pt0) cc_final: 0.6807 (pt0)
REVERT: E  234 GLU cc_start: 0.8001 (pt0) cc_final: 0.7699 (pp20)
REVERT: G   14 LYS cc_start: 0.8298 (pttm) cc_final: 0.8051 (pttm)
REVERT: G   58 GLU cc_start: 0.7988 (mp0) cc_final: 0.7568 (mp0)
REVERT: R   53 LYS cc_start: 0.7180 (mmtp) cc_final: 0.6862 (mmtp)
REVERT: R   72 VAL cc_start: 0.8295 (t) cc_final: 0.7862 (t)
REVERT: R   90 VAL cc_start: 0.8333 (t) cc_final: 0.8109 (p)
REVERT: R  132 MET cc_start: 0.5511 (mmp) cc_final: 0.4708 (mmp)
REVERT: R  185 PHE cc_start: 0.8429 (t80) cc_final: 0.8092 (t80)
REVERT: R  205 LEU cc_start: 0.7932 (tp) cc_final: 0.7701 (tt)
REVERT: R  264 MET cc_start: 0.8211 (mmm) cc_final: 0.7981 (mmm)
REVERT: R  301 TYR cc_start: 0.8238 (m-10) cc_final: 0.7627 (m-10)
  outliers start: 25
  outliers final: 19
  residues processed: 338
  average time/residue: 0.5817
  time to fit residues: 254.8302
Evaluate side-chains
  340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 321
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113132 restraints weight = 37992.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.52
r_work: 0.3361 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8959  Z= 0.149
  Angle     :  0.499   4.687  12135  Z= 0.273
  Chirality :  0.040   0.135   1377
  Planarity :  0.004   0.062   1523
  Dihedral  :  4.309  20.613   1207
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.36 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1097
  helix:  1.94 (0.27), residues: 386
  sheet:  0.08 (0.29), residues: 287
  loop : -0.42 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 211 
 HIS   0.004   0.001   HIS R 109 
 PHE   0.010   0.001   PHE E 110 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.007   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  426)
  hydrogen bonds       : angle       4.70831 ( 1194)
  covalent geometry    : bond        0.00319 ( 8959)
  covalent geometry    : angle       0.49912 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 326
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8089 (m-30) cc_final: 0.7847 (m-30)
REVERT: A   21 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7890 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7847 (tt0) cc_final: 0.7624 (tt0)
REVERT: A  204 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8123 (mm-40)
REVERT: A  214 CYS cc_start: 0.8621 (m) cc_final: 0.8409 (m)
REVERT: A  252 SER cc_start: 0.8674 (t) cc_final: 0.8307 (p)
REVERT: A  275 GLU cc_start: 0.8045 (tp30) cc_final: 0.7633 (tp30)
REVERT: A  297 GLU cc_start: 0.8229 (mp0) cc_final: 0.7745 (mp0)
REVERT: A  332 VAL cc_start: 0.8394 (t) cc_final: 0.8140 (m)
REVERT: B   10 GLU cc_start: 0.8158 (mp0) cc_final: 0.7907 (pm20)
REVERT: B   13 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: B   76 ASP cc_start: 0.7723 (m-30) cc_final: 0.7332 (m-30)
REVERT: B  110 ASN cc_start: 0.8565 (m-40) cc_final: 0.8329 (m110)
REVERT: B  134 ARG cc_start: 0.8183 (ptp-170) cc_final: 0.7909 (ptp-170)
REVERT: B  172 GLU cc_start: 0.8596 (tp30) cc_final: 0.8357 (tp30)
REVERT: B  189 SER cc_start: 0.8895 (p) cc_final: 0.8604 (t)
REVERT: B  212 ASP cc_start: 0.8354 (t0) cc_final: 0.8090 (t0)
REVERT: B  219 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8250 (ttm170)
REVERT: B  228 ASP cc_start: 0.7861 (m-30) cc_final: 0.7583 (p0)
REVERT: B  256 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8328 (mtm180)
REVERT: B  321 THR cc_start: 0.7483 (p) cc_final: 0.7205 (p)
REVERT: B  323 ASP cc_start: 0.7771 (p0) cc_final: 0.7484 (p0)
REVERT: E  220 GLU cc_start: 0.7377 (pt0) cc_final: 0.6856 (pt0)
REVERT: E  234 GLU cc_start: 0.8004 (pt0) cc_final: 0.7691 (pp20)
REVERT: G   14 LYS cc_start: 0.8274 (pttm) cc_final: 0.8037 (pttm)
REVERT: G   58 GLU cc_start: 0.8019 (mp0) cc_final: 0.7625 (mp0)
REVERT: R   53 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6798 (mmtp)
REVERT: R   72 VAL cc_start: 0.8301 (t) cc_final: 0.7791 (t)
REVERT: R   90 VAL cc_start: 0.8340 (t) cc_final: 0.8106 (p)
REVERT: R  132 MET cc_start: 0.5462 (mmp) cc_final: 0.4658 (mmp)
REVERT: R  185 PHE cc_start: 0.8419 (t80) cc_final: 0.8072 (t80)
REVERT: R  205 LEU cc_start: 0.7876 (tp) cc_final: 0.7647 (tt)
REVERT: R  301 TYR cc_start: 0.8101 (m-10) cc_final: 0.7474 (m-10)
REVERT: R  306 LEU cc_start: 0.7921 (mt) cc_final: 0.7425 (tp)
REVERT: R  310 LEU cc_start: 0.8233 (mm) cc_final: 0.7966 (mm)
  outliers start: 19
  outliers final: 18
  residues processed: 330
  average time/residue: 0.7024
  time to fit residues: 307.5370
Evaluate side-chains
  339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 321
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.130458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.111781 restraints weight = 37726.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.47
r_work: 0.3348 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8959  Z= 0.221
  Angle     :  0.520   4.613  12135  Z= 0.287
  Chirality :  0.041   0.139   1377
  Planarity :  0.004   0.069   1523
  Dihedral  :  4.351  20.765   1207
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.46 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1097
  helix:  1.92 (0.27), residues: 385
  sheet:  0.03 (0.29), residues: 288
  loop : -0.47 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R  85 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.013   0.002   PHE B 151 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.007   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  426)
  hydrogen bonds       : angle       4.71952 ( 1194)
  covalent geometry    : bond        0.00472 ( 8959)
  covalent geometry    : angle       0.52015 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  346 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 326
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8071 (m-30) cc_final: 0.7829 (m-30)
REVERT: A   21 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7913 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7908 (tt0) cc_final: 0.7644 (tt0)
REVERT: A   28 GLU cc_start: 0.8077 (tt0) cc_final: 0.7871 (tt0)
REVERT: A  204 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8150 (mm-40)
REVERT: A  214 CYS cc_start: 0.8640 (m) cc_final: 0.8433 (m)
REVERT: A  252 SER cc_start: 0.8660 (t) cc_final: 0.8296 (p)
REVERT: A  275 GLU cc_start: 0.8017 (tp30) cc_final: 0.7604 (tp30)
REVERT: A  297 GLU cc_start: 0.8236 (mp0) cc_final: 0.7743 (mp0)
REVERT: A  332 VAL cc_start: 0.8399 (t) cc_final: 0.8127 (m)
REVERT: B   10 GLU cc_start: 0.8198 (mp0) cc_final: 0.7943 (pm20)
REVERT: B   13 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: B   76 ASP cc_start: 0.7783 (m-30) cc_final: 0.7353 (m-30)
REVERT: B  110 ASN cc_start: 0.8570 (m-40) cc_final: 0.8335 (m110)
REVERT: B  172 GLU cc_start: 0.8608 (tp30) cc_final: 0.8374 (tp30)
REVERT: B  189 SER cc_start: 0.8891 (p) cc_final: 0.8617 (t)
REVERT: B  212 ASP cc_start: 0.8353 (t0) cc_final: 0.8130 (t0)
REVERT: B  219 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8250 (ttm170)
REVERT: B  256 ARG cc_start: 0.8702 (mtp85) cc_final: 0.8332 (mtm180)
REVERT: B  301 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8504 (mmtt)
REVERT: B  321 THR cc_start: 0.7492 (p) cc_final: 0.7197 (p)
REVERT: B  323 ASP cc_start: 0.7740 (p0) cc_final: 0.7471 (p0)
REVERT: B  332 TRP cc_start: 0.8396 (m-10) cc_final: 0.7102 (m-10)
REVERT: E  158 SER cc_start: 0.8742 (t) cc_final: 0.8414 (p)
REVERT: E  220 GLU cc_start: 0.7356 (pt0) cc_final: 0.6866 (pt0)
REVERT: E  234 GLU cc_start: 0.8015 (pt0) cc_final: 0.7712 (pp20)
REVERT: G   14 LYS cc_start: 0.8300 (pttm) cc_final: 0.8046 (pttm)
REVERT: G   58 GLU cc_start: 0.8018 (mp0) cc_final: 0.7597 (mp0)
REVERT: R   72 VAL cc_start: 0.8293 (t) cc_final: 0.8018 (t)
REVERT: R   79 GLU cc_start: 0.7855 (tp30) cc_final: 0.7385 (tp30)
REVERT: R   90 VAL cc_start: 0.8328 (t) cc_final: 0.8106 (p)
REVERT: R  132 MET cc_start: 0.5513 (mmp) cc_final: 0.4737 (mmp)
REVERT: R  185 PHE cc_start: 0.8441 (t80) cc_final: 0.8108 (t80)
REVERT: R  205 LEU cc_start: 0.7898 (tp) cc_final: 0.7668 (tt)
REVERT: R  301 TYR cc_start: 0.8189 (m-10) cc_final: 0.7750 (m-10)
REVERT: R  310 LEU cc_start: 0.8273 (mm) cc_final: 0.8035 (mm)
  outliers start: 20
  outliers final: 18
  residues processed: 333
  average time/residue: 0.5539
  time to fit residues: 239.5666
Evaluate side-chains
  342 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 324
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    1.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.111857 restraints weight = 38173.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.52
r_work: 0.3339 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8959  Z= 0.242
  Angle     :  0.537   6.782  12135  Z= 0.296
  Chirality :  0.041   0.142   1377
  Planarity :  0.004   0.071   1523
  Dihedral  :  4.407  20.883   1207
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.98 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1097
  helix:  1.80 (0.27), residues: 386
  sheet: -0.08 (0.29), residues: 290
  loop : -0.45 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R  85 
 HIS   0.010   0.001   HIS R 109 
 PHE   0.018   0.002   PHE E  32 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.010   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04304 (  426)
  hydrogen bonds       : angle       4.76115 ( 1194)
  covalent geometry    : bond        0.00515 ( 8959)
  covalent geometry    : angle       0.53703 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  350 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 329
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8083 (m-30) cc_final: 0.7846 (m-30)
REVERT: A   21 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7922 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7928 (tt0) cc_final: 0.7668 (tt0)
REVERT: A   28 GLU cc_start: 0.8107 (tt0) cc_final: 0.7894 (tt0)
REVERT: A  204 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8149 (mm-40)
REVERT: A  252 SER cc_start: 0.8659 (t) cc_final: 0.8290 (p)
REVERT: A  254 CYS cc_start: 0.8284 (p) cc_final: 0.7843 (p)
REVERT: A  275 GLU cc_start: 0.8030 (tp30) cc_final: 0.7614 (tp30)
REVERT: A  332 VAL cc_start: 0.8362 (t) cc_final: 0.8108 (m)
REVERT: B   13 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: B   51 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8191 (mp)
REVERT: B   76 ASP cc_start: 0.7800 (m-30) cc_final: 0.7360 (m-30)
REVERT: B  110 ASN cc_start: 0.8563 (m-40) cc_final: 0.8322 (m110)
REVERT: B  172 GLU cc_start: 0.8619 (tp30) cc_final: 0.8378 (tp30)
REVERT: B  189 SER cc_start: 0.8897 (p) cc_final: 0.8631 (t)
REVERT: B  212 ASP cc_start: 0.8302 (t0) cc_final: 0.8050 (t0)
REVERT: B  219 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8216 (ttm170)
REVERT: B  256 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8354 (mtm180)
REVERT: B  258 ASP cc_start: 0.8099 (t0) cc_final: 0.7809 (t70)
REVERT: B  301 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8511 (mmtt)
REVERT: B  321 THR cc_start: 0.7463 (p) cc_final: 0.7141 (p)
REVERT: B  323 ASP cc_start: 0.7741 (p0) cc_final: 0.7455 (p0)
REVERT: B  332 TRP cc_start: 0.8367 (m-10) cc_final: 0.7065 (m-10)
REVERT: E  220 GLU cc_start: 0.7325 (pt0) cc_final: 0.6849 (pt0)
REVERT: G   22 GLU cc_start: 0.8170 (tt0) cc_final: 0.7960 (tt0)
REVERT: G   58 GLU cc_start: 0.8020 (mp0) cc_final: 0.7600 (mp0)
REVERT: R   72 VAL cc_start: 0.8351 (t) cc_final: 0.7862 (t)
REVERT: R   79 GLU cc_start: 0.7884 (tp30) cc_final: 0.7425 (tp30)
REVERT: R   90 VAL cc_start: 0.8337 (t) cc_final: 0.8128 (p)
REVERT: R   95 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6670 (ttp80)
REVERT: R  132 MET cc_start: 0.5499 (mmp) cc_final: 0.4723 (mmp)
REVERT: R  185 PHE cc_start: 0.8454 (t80) cc_final: 0.8124 (t80)
REVERT: R  205 LEU cc_start: 0.7912 (tp) cc_final: 0.7679 (tt)
REVERT: R  301 TYR cc_start: 0.8137 (m-10) cc_final: 0.7640 (m-10)
REVERT: R  306 LEU cc_start: 0.7905 (mt) cc_final: 0.7544 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 337
  average time/residue: 0.5478
  time to fit residues: 240.6615
Evaluate side-chains
  339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 320
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 33 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0050
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.4352

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.132812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114022 restraints weight = 37845.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.53
r_work: 0.3377 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8959  Z= 0.104
  Angle     :  0.487   5.414  12135  Z= 0.261
  Chirality :  0.040   0.142   1377
  Planarity :  0.004   0.073   1523
  Dihedral  :  4.150  20.105   1207
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.34 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1097
  helix:  2.04 (0.27), residues: 388
  sheet: -0.01 (0.29), residues: 286
  loop : -0.31 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R  85 
 HIS   0.003   0.001   HIS R 109 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.009   0.001   TYR A 320 
 ARG   0.010   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  426)
  hydrogen bonds       : angle       4.51849 ( 1194)
  covalent geometry    : bond        0.00229 ( 8959)
  covalent geometry    : angle       0.48664 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  348 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 334
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8072 (m-30) cc_final: 0.7822 (m-30)
REVERT: A   21 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7876 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7905 (tt0) cc_final: 0.7676 (tt0)
REVERT: A  192 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8604 (mtmm)
REVERT: A  252 SER cc_start: 0.8670 (t) cc_final: 0.8323 (p)
REVERT: A  275 GLU cc_start: 0.8051 (tp30) cc_final: 0.7612 (tp30)
REVERT: A  297 GLU cc_start: 0.8191 (mp0) cc_final: 0.7754 (mp0)
REVERT: A  332 VAL cc_start: 0.8313 (t) cc_final: 0.8066 (m)
REVERT: B   13 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: B   76 ASP cc_start: 0.7770 (m-30) cc_final: 0.7309 (m-30)
REVERT: B  110 ASN cc_start: 0.8544 (m-40) cc_final: 0.8304 (m110)
REVERT: B  172 GLU cc_start: 0.8581 (tp30) cc_final: 0.8340 (tp30)
REVERT: B  189 SER cc_start: 0.8891 (p) cc_final: 0.8633 (t)
REVERT: B  205 ASP cc_start: 0.8066 (p0) cc_final: 0.7812 (p0)
REVERT: B  212 ASP cc_start: 0.8290 (t0) cc_final: 0.8057 (t0)
REVERT: B  219 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8211 (ttm170)
REVERT: B  321 THR cc_start: 0.7394 (p) cc_final: 0.7089 (p)
REVERT: B  323 ASP cc_start: 0.7635 (p0) cc_final: 0.7317 (p0)
REVERT: E  186 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (pt0)
REVERT: E  220 GLU cc_start: 0.7336 (pt0) cc_final: 0.6921 (pt0)
REVERT: E  234 GLU cc_start: 0.8012 (pt0) cc_final: 0.7674 (pp20)
REVERT: G   58 GLU cc_start: 0.8042 (mp0) cc_final: 0.7648 (mp0)
REVERT: R   72 VAL cc_start: 0.8305 (t) cc_final: 0.7701 (t)
REVERT: R   79 GLU cc_start: 0.7723 (tp30) cc_final: 0.7326 (tp30)
REVERT: R   95 ARG cc_start: 0.6793 (ttp80) cc_final: 0.6461 (ttp80)
REVERT: R  163 ILE cc_start: 0.8195 (pt) cc_final: 0.7889 (mm)
REVERT: R  185 PHE cc_start: 0.8449 (t80) cc_final: 0.8109 (t80)
REVERT: R  205 LEU cc_start: 0.7858 (tp) cc_final: 0.7632 (tt)
REVERT: R  207 MET cc_start: 0.8188 (mtp) cc_final: 0.7954 (ttm)
REVERT: R  301 TYR cc_start: 0.8047 (m-10) cc_final: 0.7497 (m-10)
REVERT: R  306 LEU cc_start: 0.7873 (mt) cc_final: 0.7375 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 338
  average time/residue: 0.5742
  time to fit residues: 254.9390
Evaluate side-chains
  343 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 330
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0270
   chunk 93 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    1.5444

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.131359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112613 restraints weight = 38124.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.53
r_work: 0.3353 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8959  Z= 0.203
  Angle     :  0.524   5.072  12135  Z= 0.286
  Chirality :  0.040   0.148   1377
  Planarity :  0.004   0.079   1523
  Dihedral  :  4.233  20.213   1207
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.75 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1097
  helix:  1.99 (0.27), residues: 387
  sheet: -0.07 (0.29), residues: 288
  loop : -0.36 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R  85 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.026   0.002   PHE E  32 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.010   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  426)
  hydrogen bonds       : angle       4.59780 ( 1194)
  covalent geometry    : bond        0.00438 ( 8959)
  covalent geometry    : angle       0.52394 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 325
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8085 (m-30) cc_final: 0.7846 (m-30)
REVERT: A   21 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7923 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7981 (tt0) cc_final: 0.7726 (tt0)
REVERT: A   28 GLU cc_start: 0.8111 (tt0) cc_final: 0.7904 (tt0)
REVERT: A  204 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8144 (mm-40)
REVERT: A  252 SER cc_start: 0.8661 (t) cc_final: 0.8323 (p)
REVERT: A  275 GLU cc_start: 0.8069 (tp30) cc_final: 0.7605 (tp30)
REVERT: A  297 GLU cc_start: 0.8240 (mp0) cc_final: 0.7762 (mp0)
REVERT: A  321 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8812 (p)
REVERT: A  332 VAL cc_start: 0.8338 (t) cc_final: 0.8092 (m)
REVERT: B   13 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: B   76 ASP cc_start: 0.7793 (m-30) cc_final: 0.7347 (m-30)
REVERT: B  110 ASN cc_start: 0.8544 (m-40) cc_final: 0.8313 (m110)
REVERT: B  134 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.7876 (mtm110)
REVERT: B  172 GLU cc_start: 0.8613 (tp30) cc_final: 0.8368 (tp30)
REVERT: B  189 SER cc_start: 0.8916 (p) cc_final: 0.8640 (t)
REVERT: B  212 ASP cc_start: 0.8292 (t0) cc_final: 0.8049 (t0)
REVERT: B  219 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8204 (ttm170)
REVERT: B  256 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8279 (mtm180)
REVERT: B  258 ASP cc_start: 0.8075 (t0) cc_final: 0.7737 (t70)
REVERT: B  321 THR cc_start: 0.7445 (p) cc_final: 0.7127 (p)
REVERT: B  323 ASP cc_start: 0.7657 (p0) cc_final: 0.7332 (p0)
REVERT: B  332 TRP cc_start: 0.8364 (m-10) cc_final: 0.7158 (m-10)
REVERT: E  220 GLU cc_start: 0.7362 (pt0) cc_final: 0.6950 (pt0)
REVERT: E  234 GLU cc_start: 0.8031 (pt0) cc_final: 0.7699 (pp20)
REVERT: G   22 GLU cc_start: 0.8041 (tt0) cc_final: 0.7768 (tt0)
REVERT: G   58 GLU cc_start: 0.8018 (mp0) cc_final: 0.7621 (mp0)
REVERT: R   72 VAL cc_start: 0.8328 (t) cc_final: 0.7851 (t)
REVERT: R   79 GLU cc_start: 0.7759 (tp30) cc_final: 0.7331 (tp30)
REVERT: R   95 ARG cc_start: 0.6876 (ttp80) cc_final: 0.6573 (ttp80)
REVERT: R  139 LEU cc_start: 0.7216 (tp) cc_final: 0.6922 (tp)
REVERT: R  163 ILE cc_start: 0.8225 (pt) cc_final: 0.7939 (mm)
REVERT: R  185 PHE cc_start: 0.8447 (t80) cc_final: 0.8151 (t80)
REVERT: R  205 LEU cc_start: 0.7912 (tp) cc_final: 0.7687 (tt)
REVERT: R  301 TYR cc_start: 0.8114 (m-10) cc_final: 0.7612 (m-10)
REVERT: R  306 LEU cc_start: 0.7899 (mt) cc_final: 0.7386 (tt)
  outliers start: 15
  outliers final: 13
  residues processed: 330
  average time/residue: 0.5503
  time to fit residues: 236.2254
Evaluate side-chains
  339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 325
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.131867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.113503 restraints weight = 37823.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.46
r_work: 0.3364 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8959  Z= 0.160
  Angle     :  0.508   5.100  12135  Z= 0.275
  Chirality :  0.040   0.149   1377
  Planarity :  0.004   0.079   1523
  Dihedral  :  4.207  20.035   1207
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.86 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1097
  helix:  2.01 (0.27), residues: 387
  sheet: -0.06 (0.29), residues: 285
  loop : -0.33 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  85 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.031   0.001   PHE E  32 
 TYR   0.010   0.001   TYR E  95 
 ARG   0.011   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  426)
  hydrogen bonds       : angle       4.54552 ( 1194)
  covalent geometry    : bond        0.00347 ( 8959)
  covalent geometry    : angle       0.50830 (12135)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  352 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 338
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8073 (m-30) cc_final: 0.7825 (m-30)
REVERT: A   21 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7902 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7947 (tt0) cc_final: 0.7696 (tt0)
REVERT: A  192 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8596 (mtmm)
REVERT: A  204 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8133 (mm-40)
REVERT: A  252 SER cc_start: 0.8672 (t) cc_final: 0.8326 (p)
REVERT: A  275 GLU cc_start: 0.8065 (tp30) cc_final: 0.7601 (tp30)
REVERT: A  297 GLU cc_start: 0.8230 (mp0) cc_final: 0.7764 (mp0)
REVERT: A  332 VAL cc_start: 0.8347 (t) cc_final: 0.8104 (m)
REVERT: B   13 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: B   76 ASP cc_start: 0.7777 (m-30) cc_final: 0.7333 (m-30)
REVERT: B  110 ASN cc_start: 0.8549 (m-40) cc_final: 0.8314 (m110)
REVERT: B  172 GLU cc_start: 0.8588 (tp30) cc_final: 0.8343 (tp30)
REVERT: B  189 SER cc_start: 0.8910 (p) cc_final: 0.8639 (t)
REVERT: B  205 ASP cc_start: 0.8086 (p0) cc_final: 0.7805 (p0)
REVERT: B  212 ASP cc_start: 0.8294 (t0) cc_final: 0.8041 (t0)
REVERT: B  214 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.8158 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8195 (ttm170)
REVERT: B  256 ARG cc_start: 0.8665 (mtp85) cc_final: 0.8306 (mtm180)
REVERT: B  258 ASP cc_start: 0.8077 (t0) cc_final: 0.7739 (t70)
REVERT: B  321 THR cc_start: 0.7460 (p) cc_final: 0.7120 (p)
REVERT: B  323 ASP cc_start: 0.7674 (p0) cc_final: 0.7322 (p0)
REVERT: E  186 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7932 (pt0)
REVERT: E  220 GLU cc_start: 0.7370 (pt0) cc_final: 0.6968 (pt0)
REVERT: E  234 GLU cc_start: 0.8009 (pt0) cc_final: 0.7684 (pp20)
REVERT: G   22 GLU cc_start: 0.8010 (tt0) cc_final: 0.7731 (tt0)
REVERT: G   58 GLU cc_start: 0.8012 (mp0) cc_final: 0.7606 (mp0)
REVERT: R   72 VAL cc_start: 0.8316 (t) cc_final: 0.7895 (t)
REVERT: R   79 GLU cc_start: 0.7770 (tp30) cc_final: 0.7330 (tp30)
REVERT: R  163 ILE cc_start: 0.8205 (pt) cc_final: 0.7934 (mm)
REVERT: R  185 PHE cc_start: 0.8456 (t80) cc_final: 0.8129 (t80)
REVERT: R  299 LEU cc_start: 0.8299 (tp) cc_final: 0.8041 (tp)
REVERT: R  301 TYR cc_start: 0.8136 (m-10) cc_final: 0.7682 (m-10)
  outliers start: 14
  outliers final: 12
  residues processed: 342
  average time/residue: 0.5530
  time to fit residues: 248.2379
Evaluate side-chains
  344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 331
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   chunk 31 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114597 restraints weight = 37802.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.50
r_work: 0.3383 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8959  Z= 0.106
  Angle     :  0.491   5.583  12135  Z= 0.262
  Chirality :  0.040   0.150   1377
  Planarity :  0.004   0.081   1523
  Dihedral  :  4.053  19.372   1207
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.11 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1097
  helix:  2.16 (0.28), residues: 387
  sheet: -0.05 (0.29), residues: 284
  loop : -0.26 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE A 199 
 TYR   0.008   0.001   TYR A 320 
 ARG   0.011   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  426)
  hydrogen bonds       : angle       4.41872 ( 1194)
  covalent geometry    : bond        0.00236 ( 8959)
  covalent geometry    : angle       0.49133 (12135)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10876.04 seconds
wall clock time: 186 minutes 46.64 seconds (11206.64 seconds total)