Starting phenix.real_space_refine
on Thu Mar 13 09:33:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y51_38927/03_2025/8y51_38927.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5658      2.51       5
     N    1522      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8883
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1908
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2592
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 407
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2208
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1768
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 2
  Time building chain proxies: 5.43, per 1000 atoms: 0.61
  Number of scatterers: 8883
  At special positions: 0
  Unit cell: (120.96, 88.56, 129.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1649      8.00
     N    1522      7.00
     C    5658      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      40.2% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.515A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 229 through 245
      removed outlier: 3.957A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 318
    Processing helix  chain 'A' and resid 338 through 358
      removed outlier: 3.795A  pdb=" N   ILE A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 30
      removed outlier: 3.550A  pdb=" N   CYS B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 40
      removed outlier: 3.581A  pdb=" N   ILE B  38 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 44
      removed outlier: 3.506A  pdb=" N   ALA G  32 " --> pdb=" O   LYS G  28 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TYR G  39 " --> pdb=" O   ASP G  35 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   CYS G  40 " --> pdb=" O   LEU G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 49 through 75
      removed outlier: 3.989A  pdb=" N   THR R  53 " --> pdb=" O   ALA R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 79
    Processing helix  chain 'R' and resid 80 through 108
      removed outlier: 3.594A  pdb=" N   ILE R  84 " --> pdb=" O   THR R  80 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   PHE R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE R  86 " --> pdb=" O   PRO R  82 " (cutoff:3.500A)
      Proline residue:  R 102  - end of helix
      removed outlier: 3.583A  pdb=" N   ALA R 105 " --> pdb=" O   VAL R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 116 through 150
    Processing helix  chain 'R' and resid 151 through 155
    Processing helix  chain 'R' and resid 160 through 180
      removed outlier: 3.698A  pdb=" N   THR R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL R 166 " --> pdb=" O   LEU R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 183
      No H-bonds generated for 'chain 'R' and resid 181 through 183'
    Processing helix  chain 'R' and resid 212 through 247
      Proline residue:  R 229  - end of helix
    Processing helix  chain 'R' and resid 256 through 294
      removed outlier: 3.614A  pdb=" N   LEU R 274 " --> pdb=" O   ALA R 270 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   CYS R 283 " --> pdb=" O   LEU R 279 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
    Processing helix  chain 'R' and resid 305 through 334
      removed outlier: 3.567A  pdb=" N   PHE R 309 " --> pdb=" O   SER R 305 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE R 310 " --> pdb=" O   ALA R 306 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASN R 322 " --> pdb=" O   LEU R 318 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   SER R 323 " --> pdb=" O   ALA R 319 " (cutoff:3.500A)
      Proline residue:  R 327  - end of helix
      removed outlier: 3.726A  pdb=" N   LEU R 330 " --> pdb=" O   ASN R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 349
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 52 through 55
      removed outlier: 3.680A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 55'
    Processing helix  chain 'E' and resid 73 through 75
      No H-bonds generated for 'chain 'E' and resid 73 through 75'
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.522A  pdb=" N   THR E  90 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.786A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.823A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.966A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B  54 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.708A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B  76 " --> pdb=" O   HIS B  67 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER B  77 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B  85 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.636A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   CYS B 119 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER B 127 " --> pdb=" O   CYS B 119 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 3.779A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.450A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER B 206 " --> pdb=" O   LYS B 214 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS B 214 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.513A  pdb=" N   ARG B 256 " --> pdb=" O   THR B 248 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP B 259 " --> pdb=" O   GLN B 264 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.854A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR B 294 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ASN B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   CYS B 299 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   VAL B 312 " --> pdb=" O   CYS B 299 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL B 301 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.453A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.759A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1473
        1.32 -     1.44: 2461
        1.44 -     1.57: 5055
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 9064
  Sorted by residual:
  bond pdb=" C   LYS R 167 "
       pdb=" O   LYS R 167 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.037 1.19e-02 7.06e+03 9.71e+00
  bond pdb=" N   ALA R 110 "
       pdb=" CA  ALA R 110 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.28e+00
  bond pdb=" N   GLU B   8 "
       pdb=" CA  GLU B   8 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.08e+00
  bond pdb=" N   THR G   5 "
       pdb=" CA  THR G   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
  bond pdb=" N   LEU A   5 "
       pdb=" CA  LEU A   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  ... (remaining 9059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 12101
        1.34 -     2.69: 129
        2.69 -     4.03: 38
        4.03 -     5.37: 2
        5.37 -     6.72: 3
  Bond angle restraints: 12273
  Sorted by residual:
  angle pdb=" N   GLY R 112 "
        pdb=" CA  GLY R 112 "
        pdb=" C   GLY R 112 "
      ideal   model   delta    sigma   weight residual
     112.45  119.17   -6.72 1.55e+00 4.16e-01 1.88e+01
  angle pdb=" CB  LYS R 167 "
        pdb=" CG  LYS R 167 "
        pdb=" CD  LYS R 167 "
      ideal   model   delta    sigma   weight residual
     111.30  117.71   -6.41 2.30e+00 1.89e-01 7.77e+00
  angle pdb=" N   VAL A 334 "
        pdb=" CA  VAL A 334 "
        pdb=" C   VAL A 334 "
      ideal   model   delta    sigma   weight residual
     113.10  110.40    2.70 9.70e-01 1.06e+00 7.76e+00
  angle pdb=" N   ALA R 110 "
        pdb=" CA  ALA R 110 "
        pdb=" C   ALA R 110 "
      ideal   model   delta    sigma   weight residual
     110.80  116.58   -5.78 2.13e+00 2.20e-01 7.37e+00
  angle pdb=" N   ILE R 228 "
        pdb=" CA  ILE R 228 "
        pdb=" C   ILE R 228 "
      ideal   model   delta    sigma   weight residual
     112.35  109.26    3.09 1.20e+00 6.94e-01 6.62e+00
  ... (remaining 12268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 5237
       17.00 -    34.00: 124
       34.00 -    51.00: 23
       51.00 -    68.00: 7
       68.00 -    84.99: 3
  Dihedral angle restraints: 5394
    sinusoidal: 2106
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" N   PHE R 225 "
           pdb=" CA  PHE R 225 "
           pdb=" CB  PHE R 225 "
           pdb=" CG  PHE R 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.75  -58.75     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   PHE B 239 "
           pdb=" CA  PHE B 239 "
           pdb=" CB  PHE B 239 "
           pdb=" CG  PHE B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.76  -55.24     3      1.50e+01 4.44e-03 9.33e+00
  dihedral pdb=" N   ARG E 191 "
           pdb=" CA  ARG E 191 "
           pdb=" CB  ARG E 191 "
           pdb=" CG  ARG E 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.52   51.52     3      1.50e+01 4.44e-03 9.02e+00
  ... (remaining 5391 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1100
       0.036 -    0.073: 198
       0.073 -    0.109: 65
       0.109 -    0.145: 36
       0.145 -    0.182: 1
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CA  ALA R 110 "
            pdb=" N   ALA R 110 "
            pdb=" C   ALA R 110 "
            pdb=" CB  ALA R 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.30    0.18 2.00e-01 2.50e+01 8.26e-01
  chirality pdb=" CA  ILE B 237 "
            pdb=" N   ILE B 237 "
            pdb=" C   ILE B 237 "
            pdb=" CB  ILE B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE R 251 "
            pdb=" N   ILE R 251 "
            pdb=" C   ILE R 251 "
            pdb=" CB  ILE R 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 1397 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO E 236 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 251 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.37e-01
        pdb=" N   PRO R 252 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO R 252 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 252 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 109 "   -0.004 2.00e-02 2.50e+03   8.51e-03 7.25e-01
        pdb=" C   LEU R 109 "    0.015 2.00e-02 2.50e+03
        pdb=" O   LEU R 109 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   ALA R 110 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 121
        2.62 -     3.19: 8291
        3.19 -     3.76: 13624
        3.76 -     4.33: 18993
        4.33 -     4.90: 31923
  Nonbonded interactions: 72952
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  79 "
            pdb=" OD1 ASP B  81 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" O   LEU R 318 "
            pdb=" OG  SER R 321 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OG  SER G  56 "
            pdb=" OE1 GLU G  57 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" CG2 THR R  80 "
            pdb=" OD1 ASN R  83 "
     model   vdw
     2.134 3.460
  nonbonded pdb=" OE2 GLU A 207 "
            pdb=" NH1 ARG A 209 "
     model   vdw
     2.163 3.120
  ... (remaining 72947 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:                  0.010
  Normalize map: mean=0, sd=1:             0.350
  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:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.300
  Find NCS groups from input model:        0.090
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9064  Z= 0.133
  Angle     :  0.426   6.718  12273  Z= 0.263
  Chirality :  0.038   0.182   1400
  Planarity :  0.002   0.051   1548
  Dihedral  :  8.227  84.994   3268
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  0.81 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.95 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.23), residues: 1110
  helix:  0.74 (0.24), residues: 393
  sheet: -1.04 (0.29), residues: 285
  loop : -1.50 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 211 
 HIS   0.002   0.000   HIS R 294 
 PHE   0.007   0.001   PHE R 115 
 TYR   0.005   0.001   TYR E 235 
 ARG   0.002   0.000   ARG A  15 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 314
  time to evaluate  : 0.851 
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  190 GLN cc_start: 0.6767 (tt0) cc_final: 0.6243 (tt0)
REVERT: B  294 TYR cc_start: 0.8107 (m-80) cc_final: 0.7753 (m-80)
REVERT: G   39 TYR cc_start: 0.6502 (t80) cc_final: 0.6268 (t80)
REVERT: E   18 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7773 (ttmm)
  outliers start: 2
  outliers final: 1
  residues processed: 316
  average time/residue: 0.2941
  time to fit residues: 120.7330
Evaluate side-chains
  185 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  225 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 44 optimal weight:    0.1980
   chunk 87 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    3.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
A 359 ASN
B  67 HIS
B 235 ASN
B 271 HIS
B 300 ASN
B 345 ASN
** R  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  83 ASN
E  38 GLN
E  76 ASN
E 183 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.081221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.060678 restraints weight = 26215.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 4.02
r_work: 0.2915 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9064  Z= 0.368
  Angle     :  0.685   7.272  12273  Z= 0.353
  Chirality :  0.045   0.182   1400
  Planarity :  0.005   0.059   1548
  Dihedral  :  4.299  56.960   1228
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.61 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.25), residues: 1110
  helix:  1.52 (0.25), residues: 392
  sheet: -0.43 (0.30), residues: 275
  loop : -0.36 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 174 
 HIS   0.007   0.002   HIS G  43 
 PHE   0.016   0.002   PHE B 258 
 TYR   0.027   0.002   TYR E 235 
 ARG   0.007   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 179
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.9127 (t70) cc_final: 0.8878 (t70)
REVERT: B   27 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8270 (ttt180)
REVERT: B   37 GLN cc_start: 0.9433 (mt0) cc_final: 0.9154 (mp10)
REVERT: B  220 GLU cc_start: 0.8443 (mp0) cc_final: 0.7974 (mp0)
REVERT: B  239 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9071 (m-80)
REVERT: B  264 GLN cc_start: 0.8424 (tt0) cc_final: 0.8035 (mt0)
REVERT: B  267 MET cc_start: 0.8438 (tpp) cc_final: 0.7844 (mtp)
REVERT: B  280 SER cc_start: 0.9226 (t) cc_final: 0.8958 (m)
REVERT: B  285 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8844 (mtpp)
REVERT: B  344 TRP cc_start: 0.8587 (m100) cc_final: 0.8301 (m-10)
REVERT: R  155 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8087 (ptm-80)
REVERT: E   18 LYS cc_start: 0.9521 (ttpt) cc_final: 0.8940 (ttmm)
REVERT: E  137 ASP cc_start: 0.8797 (p0) cc_final: 0.8511 (p0)
REVERT: E  140 MET cc_start: 0.8565 (mmm) cc_final: 0.8092 (mmm)
REVERT: E  153 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: E  186 GLN cc_start: 0.8841 (tt0) cc_final: 0.8512 (tt0)
  outliers start: 36
  outliers final: 23
  residues processed: 206
  average time/residue: 0.2326
  time to fit residues: 64.8543
Evaluate side-chains
  174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  269 ILE
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain E residue  235 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 109 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 197 HIS
A 359 ASN
B  22 GLN
B  49 GLN
B 160 ASN
R  83 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.081147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.060659 restraints weight = 26675.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 4.06
r_work: 0.2915 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9064  Z= 0.225
  Angle     :  0.589   7.520  12273  Z= 0.304
  Chirality :  0.042   0.193   1400
  Planarity :  0.004   0.045   1548
  Dihedral  :  4.172  56.489   1228
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.05 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.25), residues: 1110
  helix:  1.84 (0.26), residues: 395
  sheet: -0.19 (0.31), residues: 270
  loop : -0.19 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 174 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.029   0.001   TYR E 235 
 ARG   0.008   0.000   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.915 
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: B  135 GLU cc_start: 0.8578 (mp0) cc_final: 0.8168 (mp0)
REVERT: B  220 GLU cc_start: 0.8349 (mp0) cc_final: 0.8079 (mp0)
REVERT: B  228 THR cc_start: 0.8874 (p) cc_final: 0.8620 (t)
REVERT: B  239 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9060 (m-80)
REVERT: B  264 GLN cc_start: 0.8454 (tt0) cc_final: 0.8148 (tt0)
REVERT: B  267 MET cc_start: 0.8438 (tpp) cc_final: 0.8219 (ttm)
REVERT: B  280 SER cc_start: 0.9210 (t) cc_final: 0.8939 (m)
REVERT: B  285 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8862 (mtpp)
REVERT: B  344 TRP cc_start: 0.8639 (m100) cc_final: 0.8346 (m-10)
REVERT: G   41 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9043 (mm-30)
REVERT: R  155 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8040 (ptm-80)
REVERT: E   18 LYS cc_start: 0.9482 (ttpt) cc_final: 0.8911 (ttmm)
REVERT: E   67 PHE cc_start: 0.8785 (m-10) cc_final: 0.8339 (m-10)
REVERT: E   82 MET cc_start: 0.9275 (mmm) cc_final: 0.8845 (mmm)
REVERT: E  137 ASP cc_start: 0.8776 (p0) cc_final: 0.8478 (p0)
REVERT: E  140 MET cc_start: 0.8470 (mmm) cc_final: 0.7858 (mmm)
REVERT: E  153 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: E  186 GLN cc_start: 0.8818 (tt0) cc_final: 0.8596 (tt0)
REVERT: E  218 ARG cc_start: 0.8834 (mtm110) cc_final: 0.8472 (mtm110)
  outliers start: 28
  outliers final: 20
  residues processed: 193
  average time/residue: 0.2196
  time to fit residues: 57.4334
Evaluate side-chains
  168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain E residue   76 ASN
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  235 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 102 optimal weight:   10.0000
   chunk 96 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 GLN
B  49 GLN
R 294 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.080010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059336 restraints weight = 26388.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 4.03
r_work: 0.2881 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9064  Z= 0.241
  Angle     :  0.595  10.070  12273  Z= 0.304
  Chirality :  0.042   0.186   1400
  Planarity :  0.004   0.055   1548
  Dihedral  :  4.215  56.256   1228
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.80 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.96 (0.26), residues: 1110
  helix:  1.97 (0.26), residues: 394
  sheet:  0.01 (0.31), residues: 270
  loop : -0.07 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 174 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.018   0.001   PHE R 222 
 TYR   0.027   0.001   TYR E 235 
 ARG   0.010   0.000   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6873 (tm-30)
REVERT: B   27 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8261 (ttt180)
REVERT: B  135 GLU cc_start: 0.8632 (mp0) cc_final: 0.8287 (mp0)
REVERT: B  222 MET cc_start: 0.8199 (ppp) cc_final: 0.7596 (pmm)
REVERT: B  228 THR cc_start: 0.8831 (p) cc_final: 0.8532 (t)
REVERT: B  239 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8998 (m-80)
REVERT: B  267 MET cc_start: 0.8447 (tpp) cc_final: 0.7996 (mtp)
REVERT: B  280 SER cc_start: 0.9299 (t) cc_final: 0.8956 (m)
REVERT: B  285 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8860 (mtpp)
REVERT: B  344 TRP cc_start: 0.8708 (m100) cc_final: 0.8343 (m-10)
REVERT: G   26 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7666 (ttm170)
REVERT: G   37 MET cc_start: 0.8930 (ttp) cc_final: 0.7736 (tmm)
REVERT: G   41 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: R   78 MET cc_start: 0.8708 (mmm) cc_final: 0.8112 (mmm)
REVERT: R   93 ASP cc_start: 0.8543 (m-30) cc_final: 0.8057 (t0)
REVERT: R  154 GLU cc_start: 0.8435 (mp0) cc_final: 0.8233 (mp0)
REVERT: R  268 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8031 (ttm-80)
REVERT: R  337 PHE cc_start: 0.9068 (t80) cc_final: 0.8702 (t80)
REVERT: E   18 LYS cc_start: 0.9512 (ttpt) cc_final: 0.8993 (ttmm)
REVERT: E   82 MET cc_start: 0.9263 (mmm) cc_final: 0.8841 (mmm)
REVERT: E  137 ASP cc_start: 0.8784 (p0) cc_final: 0.8497 (p0)
REVERT: E  140 MET cc_start: 0.8432 (mmm) cc_final: 0.8034 (mmm)
REVERT: E  153 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7957 (tm-30)
REVERT: E  186 GLN cc_start: 0.8828 (tt0) cc_final: 0.8617 (tt0)
  outliers start: 30
  outliers final: 21
  residues processed: 180
  average time/residue: 0.2218
  time to fit residues: 54.1891
Evaluate side-chains
  168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  268 ARG
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue   76 ASN
Chi-restraints excluded: chain E residue  150 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0770
   chunk 5 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.080986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.060815 restraints weight = 26262.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 4.02
r_work: 0.2917 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9064  Z= 0.176
  Angle     :  0.572   8.803  12273  Z= 0.293
  Chirality :  0.041   0.178   1400
  Planarity :  0.004   0.050   1548
  Dihedral  :  4.109  54.847   1228
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.52 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1110
  helix:  2.02 (0.26), residues: 394
  sheet:  0.12 (0.31), residues: 277
  loop :  0.08 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 174 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.024   0.001   TYR E 235 
 ARG   0.011   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8883 (m-30) cc_final: 0.8411 (m-30)
REVERT: A  186 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6892 (tm-30)
REVERT: A  284 ARG cc_start: 0.9052 (mtm110) cc_final: 0.8828 (ptm-80)
REVERT: B   27 ARG cc_start: 0.9021 (ttm170) cc_final: 0.8418 (mtt180)
REVERT: B  135 GLU cc_start: 0.8643 (mp0) cc_final: 0.8385 (mp0)
REVERT: B  220 GLU cc_start: 0.8676 (mp0) cc_final: 0.8288 (pm20)
REVERT: B  222 MET cc_start: 0.8282 (ppp) cc_final: 0.7391 (ppp)
REVERT: B  225 GLN cc_start: 0.8752 (mt0) cc_final: 0.8445 (mt0)
REVERT: B  228 THR cc_start: 0.8788 (p) cc_final: 0.8502 (t)
REVERT: B  239 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9059 (m-80)
REVERT: B  267 MET cc_start: 0.8401 (tpp) cc_final: 0.8062 (mtp)
REVERT: B  280 SER cc_start: 0.9241 (t) cc_final: 0.8911 (m)
REVERT: B  344 TRP cc_start: 0.8657 (m100) cc_final: 0.8452 (m100)
REVERT: G   37 MET cc_start: 0.8938 (ttp) cc_final: 0.7678 (tmm)
REVERT: G   41 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8042 (mm-30)
REVERT: R  154 GLU cc_start: 0.8304 (mp0) cc_final: 0.7857 (mp0)
REVERT: R  255 GLU cc_start: 0.8496 (tp30) cc_final: 0.8294 (tm-30)
REVERT: R  268 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7861 (ttm-80)
REVERT: E   18 LYS cc_start: 0.9486 (ttpt) cc_final: 0.8975 (ttmm)
REVERT: E   82 MET cc_start: 0.9275 (mmm) cc_final: 0.9004 (mmm)
REVERT: E  108 ASP cc_start: 0.9109 (p0) cc_final: 0.8753 (p0)
REVERT: E  137 ASP cc_start: 0.8794 (p0) cc_final: 0.8535 (p0)
REVERT: E  140 MET cc_start: 0.8410 (mmm) cc_final: 0.8094 (mmm)
REVERT: E  153 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: E  218 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8265 (mtm110)
REVERT: E  220 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8217 (mp0)
REVERT: E  223 ASP cc_start: 0.7508 (m-30) cc_final: 0.7149 (m-30)
REVERT: E  230 MET cc_start: 0.9091 (ttp) cc_final: 0.8781 (tmm)
  outliers start: 32
  outliers final: 21
  residues processed: 184
  average time/residue: 0.2335
  time to fit residues: 57.5678
Evaluate side-chains
  170 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  268 ARG
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue   76 ASN
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.078522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.058176 restraints weight = 26350.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 3.95
r_work: 0.2851 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9064  Z= 0.269
  Angle     :  0.615  12.993  12273  Z= 0.312
  Chirality :  0.042   0.373   1400
  Planarity :  0.004   0.053   1548
  Dihedral  :  4.219  54.575   1228
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.55 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.26), residues: 1110
  helix:  1.97 (0.25), residues: 402
  sheet:  0.03 (0.31), residues: 279
  loop :  0.11 (0.32), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.031   0.001   TYR E 235 
 ARG   0.010   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6895 (tm-30)
REVERT: B  135 GLU cc_start: 0.8697 (mp0) cc_final: 0.8487 (mp0)
REVERT: B  222 MET cc_start: 0.8374 (ppp) cc_final: 0.7728 (pmm)
REVERT: B  228 THR cc_start: 0.8820 (p) cc_final: 0.8527 (t)
REVERT: B  239 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8773 (m-80)
REVERT: B  267 MET cc_start: 0.8435 (tpp) cc_final: 0.8174 (mtp)
REVERT: B  280 SER cc_start: 0.9336 (t) cc_final: 0.8953 (m)
REVERT: B  285 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8562 (ttmm)
REVERT: B  344 TRP cc_start: 0.8755 (m100) cc_final: 0.8377 (m-10)
REVERT: G   20 MET cc_start: 0.9495 (mmm) cc_final: 0.8529 (mmm)
REVERT: R   93 ASP cc_start: 0.8355 (m-30) cc_final: 0.7990 (t0)
REVERT: R  154 GLU cc_start: 0.8464 (mp0) cc_final: 0.7984 (mp0)
REVERT: R  268 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7819 (ttm-80)
REVERT: R  337 PHE cc_start: 0.8999 (t80) cc_final: 0.8597 (t80)
REVERT: E   18 LYS cc_start: 0.9507 (ttpt) cc_final: 0.8996 (ttmm)
REVERT: E   82 MET cc_start: 0.9308 (mmm) cc_final: 0.9024 (mmm)
REVERT: E  137 ASP cc_start: 0.8774 (p0) cc_final: 0.8523 (p0)
REVERT: E  140 MET cc_start: 0.8463 (mmm) cc_final: 0.8102 (mmm)
REVERT: E  153 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: E  218 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8455 (mtm110)
REVERT: E  220 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8395 (mm-30)
REVERT: E  223 ASP cc_start: 0.7550 (m-30) cc_final: 0.7127 (m-30)
REVERT: E  230 MET cc_start: 0.9086 (ttp) cc_final: 0.8823 (tmm)
  outliers start: 34
  outliers final: 25
  residues processed: 178
  average time/residue: 0.2348
  time to fit residues: 56.0949
Evaluate side-chains
  177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  268 ARG
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue   76 ASN
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 190 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.078407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.058111 restraints weight = 26170.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 3.95
r_work: 0.2854 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9064  Z= 0.228
  Angle     :  0.620   9.676  12273  Z= 0.314
  Chirality :  0.041   0.169   1400
  Planarity :  0.004   0.051   1548
  Dihedral  :  4.203  54.410   1228
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.37 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.26), residues: 1110
  helix:  2.15 (0.25), residues: 395
  sheet:  0.09 (0.31), residues: 279
  loop :  0.15 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.002   0.001   HIS E 167 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.028   0.001   TYR E 235 
 ARG   0.012   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.941 
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: A  186 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6828 (tm-30)
REVERT: A  284 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8897 (ptm-80)
REVERT: B   18 GLN cc_start: 0.9642 (OUTLIER) cc_final: 0.9441 (pp30)
REVERT: B  228 THR cc_start: 0.8784 (p) cc_final: 0.8468 (t)
REVERT: B  239 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9017 (m-80)
REVERT: B  267 MET cc_start: 0.8279 (tpp) cc_final: 0.8037 (mtt)
REVERT: B  280 SER cc_start: 0.9305 (t) cc_final: 0.8951 (m)
REVERT: B  285 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8714 (ttmm)
REVERT: B  299 CYS cc_start: 0.8671 (t) cc_final: 0.8418 (m)
REVERT: B  344 TRP cc_start: 0.8765 (m100) cc_final: 0.8381 (m-10)
REVERT: R   93 ASP cc_start: 0.8394 (m-30) cc_final: 0.8031 (t0)
REVERT: R  154 GLU cc_start: 0.8469 (mp0) cc_final: 0.8018 (mp0)
REVERT: R  268 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (ttm-80)
REVERT: E   18 LYS cc_start: 0.9523 (ttpt) cc_final: 0.9044 (ttmm)
REVERT: E   82 MET cc_start: 0.9216 (mmm) cc_final: 0.8821 (mmm)
REVERT: E  108 ASP cc_start: 0.9089 (p0) cc_final: 0.8811 (p0)
REVERT: E  137 ASP cc_start: 0.8778 (p0) cc_final: 0.8535 (p0)
REVERT: E  140 MET cc_start: 0.8471 (mmm) cc_final: 0.8065 (mmm)
REVERT: E  153 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: E  186 GLN cc_start: 0.8895 (tt0) cc_final: 0.8409 (pt0)
REVERT: E  218 ARG cc_start: 0.8889 (mtm110) cc_final: 0.8440 (mtm110)
REVERT: E  220 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8373 (mm-30)
REVERT: E  223 ASP cc_start: 0.7672 (m-30) cc_final: 0.7267 (m-30)
REVERT: E  230 MET cc_start: 0.9055 (ttp) cc_final: 0.8825 (tmm)
  outliers start: 32
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2363
  time to fit residues: 58.4091
Evaluate side-chains
  180 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  268 ARG
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue   76 ASN
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.077086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.056380 restraints weight = 26627.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 3.97
r_work: 0.2812 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9064  Z= 0.296
  Angle     :  0.679  11.105  12273  Z= 0.342
  Chirality :  0.042   0.186   1400
  Planarity :  0.004   0.052   1548
  Dihedral  :  4.392  54.785   1228
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.16 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.26), residues: 1110
  helix:  2.16 (0.25), residues: 396
  sheet:  0.36 (0.33), residues: 257
  loop :  0.08 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 217 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.036   0.001   TYR E 235 
 ARG   0.014   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.6890 (tm-30)
REVERT: B   50 MET cc_start: 0.8720 (mmp) cc_final: 0.8234 (mmm)
REVERT: B  135 GLU cc_start: 0.8851 (mp0) cc_final: 0.8627 (mp0)
REVERT: B  160 ASN cc_start: 0.8355 (t0) cc_final: 0.8053 (t0)
REVERT: B  239 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8533 (m-80)
REVERT: B  280 SER cc_start: 0.9313 (t) cc_final: 0.8938 (m)
REVERT: B  285 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8653 (ttmm)
REVERT: B  344 TRP cc_start: 0.8853 (m100) cc_final: 0.8497 (m-10)
REVERT: R   93 ASP cc_start: 0.8427 (m-30) cc_final: 0.8042 (t0)
REVERT: R  154 GLU cc_start: 0.8527 (mp0) cc_final: 0.8067 (mp0)
REVERT: R  268 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8066 (ttm-80)
REVERT: E   18 LYS cc_start: 0.9539 (ttpt) cc_final: 0.9046 (ttmm)
REVERT: E   72 ASP cc_start: 0.7933 (t70) cc_final: 0.7730 (t70)
REVERT: E   82 MET cc_start: 0.9255 (mmm) cc_final: 0.8746 (mmm)
REVERT: E  108 ASP cc_start: 0.9100 (p0) cc_final: 0.8876 (p0)
REVERT: E  137 ASP cc_start: 0.8810 (p0) cc_final: 0.8581 (p0)
REVERT: E  140 MET cc_start: 0.8468 (mmm) cc_final: 0.8063 (mmm)
REVERT: E  153 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: E  186 GLN cc_start: 0.8924 (tt0) cc_final: 0.8433 (pt0)
REVERT: E  218 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8470 (mtm110)
REVERT: E  220 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: E  223 ASP cc_start: 0.7580 (m-30) cc_final: 0.7203 (m-30)
REVERT: E  230 MET cc_start: 0.9054 (ttp) cc_final: 0.8823 (tmm)
  outliers start: 35
  outliers final: 30
  residues processed: 185
  average time/residue: 0.2331
  time to fit residues: 57.9608
Evaluate side-chains
  183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain G residue   35 ASP
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue   87 THR
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  166 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  268 ARG
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.078482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.058217 restraints weight = 26477.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 3.97
r_work: 0.2855 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9064  Z= 0.198
  Angle     :  0.668  12.541  12273  Z= 0.333
  Chirality :  0.041   0.154   1400
  Planarity :  0.004   0.060   1548
  Dihedral  :  4.332  54.237   1228
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.09 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1110
  helix:  2.14 (0.25), residues: 395
  sheet:  0.32 (0.32), residues: 269
  loop :  0.05 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.002   0.001   HIS A 197 
 PHE   0.023   0.001   PHE A 189 
 TYR   0.034   0.001   TYR E 235 
 ARG   0.014   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8849 (m-30)
REVERT: A   18 MET cc_start: 0.8785 (mmm) cc_final: 0.8563 (mmm)
REVERT: A   51 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9271 (mmmm)
REVERT: A  186 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6870 (tm-30)
REVERT: A  284 ARG cc_start: 0.9129 (mtm110) cc_final: 0.8889 (ptm-80)
REVERT: B   27 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8063 (ttt180)
REVERT: B   37 GLN cc_start: 0.9524 (mt0) cc_final: 0.9214 (mp10)
REVERT: B   50 MET cc_start: 0.8701 (mmp) cc_final: 0.8209 (mmm)
REVERT: B  177 GLU cc_start: 0.9154 (pm20) cc_final: 0.8947 (pm20)
REVERT: B  220 GLU cc_start: 0.8177 (pm20) cc_final: 0.7783 (pm20)
REVERT: B  239 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8801 (m-80)
REVERT: B  280 SER cc_start: 0.9250 (t) cc_final: 0.8914 (m)
REVERT: B  285 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8558 (ttmm)
REVERT: B  306 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8276 (mmtt)
REVERT: B  344 TRP cc_start: 0.8768 (m100) cc_final: 0.8483 (m-10)
REVERT: R   93 ASP cc_start: 0.8341 (m-30) cc_final: 0.7967 (t0)
REVERT: R  154 GLU cc_start: 0.8434 (mp0) cc_final: 0.7988 (mp0)
REVERT: R  337 PHE cc_start: 0.8911 (t80) cc_final: 0.8508 (t80)
REVERT: E   18 LYS cc_start: 0.9526 (ttpt) cc_final: 0.9046 (ttmm)
REVERT: E   82 MET cc_start: 0.9196 (mmm) cc_final: 0.8720 (mmm)
REVERT: E  108 ASP cc_start: 0.9045 (p0) cc_final: 0.8747 (p0)
REVERT: E  116 LEU cc_start: 0.9302 (tp) cc_final: 0.9074 (tt)
REVERT: E  137 ASP cc_start: 0.8794 (p0) cc_final: 0.8572 (p0)
REVERT: E  140 MET cc_start: 0.8461 (mmm) cc_final: 0.8059 (mmm)
REVERT: E  153 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: E  186 GLN cc_start: 0.8922 (tt0) cc_final: 0.8504 (pt0)
REVERT: E  218 ARG cc_start: 0.8893 (mtm110) cc_final: 0.8463 (mtm110)
REVERT: E  220 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8484 (mm-30)
REVERT: E  223 ASP cc_start: 0.7590 (m-30) cc_final: 0.7224 (m-30)
REVERT: E  230 MET cc_start: 0.9006 (ttp) cc_final: 0.8806 (tmm)
  outliers start: 28
  outliers final: 24
  residues processed: 180
  average time/residue: 0.2250
  time to fit residues: 54.6863
Evaluate side-chains
  179 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.077005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.056644 restraints weight = 26536.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 3.93
r_work: 0.2819 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9064  Z= 0.291
  Angle     :  0.711  11.691  12273  Z= 0.356
  Chirality :  0.042   0.168   1400
  Planarity :  0.004   0.064   1548
  Dihedral  :  4.451  54.408   1228
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.60 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1110
  helix:  2.14 (0.25), residues: 396
  sheet:  0.35 (0.33), residues: 255
  loop :  0.04 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 174 
 HIS   0.003   0.001   HIS E 167 
 PHE   0.024   0.001   PHE A 189 
 TYR   0.045   0.001   TYR E 235 
 ARG   0.015   0.001   ARG E 160 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8830 (mmm) cc_final: 0.8608 (mmm)
REVERT: A   51 LYS cc_start: 0.9520 (mmmt) cc_final: 0.9289 (mmmm)
REVERT: A  186 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6880 (tm-30)
REVERT: A  284 ARG cc_start: 0.9141 (mtm110) cc_final: 0.8892 (ptm-80)
REVERT: B   49 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8595 (mm-40)
REVERT: B   50 MET cc_start: 0.8814 (mmp) cc_final: 0.8205 (mmm)
REVERT: B  220 GLU cc_start: 0.8193 (pm20) cc_final: 0.7810 (pm20)
REVERT: B  239 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8594 (m-80)
REVERT: B  280 SER cc_start: 0.9334 (t) cc_final: 0.8950 (m)
REVERT: B  285 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8515 (ttmm)
REVERT: B  344 TRP cc_start: 0.8830 (m100) cc_final: 0.8461 (m-10)
REVERT: R   93 ASP cc_start: 0.8399 (m-30) cc_final: 0.7989 (t0)
REVERT: R  154 GLU cc_start: 0.8483 (mp0) cc_final: 0.8035 (mp0)
REVERT: E   18 LYS cc_start: 0.9545 (ttpt) cc_final: 0.9066 (ttmm)
REVERT: E   81 GLN cc_start: 0.8857 (mm-40) cc_final: 0.7853 (tp-100)
REVERT: E   82 MET cc_start: 0.9236 (mmm) cc_final: 0.8864 (mmm)
REVERT: E  108 ASP cc_start: 0.9067 (p0) cc_final: 0.8818 (p0)
REVERT: E  116 LEU cc_start: 0.9313 (tp) cc_final: 0.9039 (tt)
REVERT: E  137 ASP cc_start: 0.8795 (p0) cc_final: 0.8568 (p0)
REVERT: E  140 MET cc_start: 0.8493 (mmm) cc_final: 0.8081 (mmm)
REVERT: E  153 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: E  186 GLN cc_start: 0.8946 (tt0) cc_final: 0.8479 (pt0)
REVERT: E  218 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8457 (mtm110)
REVERT: E  220 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8436 (mm-30)
REVERT: E  223 ASP cc_start: 0.7594 (m-30) cc_final: 0.7237 (m-30)
REVERT: E  230 MET cc_start: 0.9053 (ttp) cc_final: 0.8827 (tmm)
  outliers start: 27
  outliers final: 24
  residues processed: 171
  average time/residue: 0.2196
  time to fit residues: 51.1615
Evaluate side-chains
  177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain G residue   49 LEU
Chi-restraints excluded: chain R residue  133 VAL
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  175 SER
Chi-restraints excluded: chain R residue  221 CYS
Chi-restraints excluded: chain R residue  225 PHE
Chi-restraints excluded: chain R residue  231 SER
Chi-restraints excluded: chain R residue  234 SER
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  275 VAL
Chi-restraints excluded: chain R residue  291 TYR
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  314 PHE
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0980
   chunk 3 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.078331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.058132 restraints weight = 26408.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.97
r_work: 0.2858 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9064  Z= 0.214
  Angle     :  0.714  14.059  12273  Z= 0.358
  Chirality :  0.043   0.310   1400
  Planarity :  0.004   0.065   1548
  Dihedral  :  4.402  53.796   1228
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.01 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.26), residues: 1110
  helix:  2.13 (0.25), residues: 395
  sheet:  0.36 (0.33), residues: 257
  loop :  0.01 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 174 
 HIS   0.002   0.001   HIS E  34 
 PHE   0.033   0.001   PHE R 222 
 TYR   0.044   0.001   TYR E 235 
 ARG   0.015   0.001   ARG E 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5370.78 seconds
wall clock time: 93 minutes 56.98 seconds (5636.98 seconds total)