Starting phenix.real_space_refine
on Thu Mar 13 07:47:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iu2_35714/03_2025/8iu2_35714.cif"
  }
  resolution = 3.35
  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=   0.001 sd=   0.012
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      67      5.16       5
     C    5591      2.51       5
     N    1481      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8734
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2338
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 280}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1589
          Classifications: {'peptide': 209}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 206}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 96
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 62
    Chain: "B"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2598
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1751
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   TRP R 177 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CH2 TRP R 177 " occ=0.50
    residue:
      pdb=" N   PHE R 329 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE R 329 " occ=0.50
  Time building chain proxies: 5.89, per 1000 atoms: 0.67
  Number of scatterers: 8734
  At special positions: 0
  Unit cell: (89.512, 123.58, 128.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    1595      8.00
     N    1481      7.00
     C    5591      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 126 " - pdb=" SG  CYS R 203 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 969.7 milliseconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 17 sheets defined
      36.1% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'R' and resid 49 through 81
      removed outlier: 3.768A  pdb=" N   TYR R  53 " --> pdb=" O   PRO R  49 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL R  74 " --> pdb=" O   THR R  70 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 117
      removed outlier: 3.525A  pdb=" N   VAL R  93 " --> pdb=" O   ASN R  89 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER R 107 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE R 109 " --> pdb=" O   ILE R 105 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   SER R 110 " --> pdb=" O   ALA R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 157
    Processing helix  chain 'R' and resid 165 through 185
      removed outlier: 4.010A  pdb=" N   ALA R 169 " --> pdb=" O   ASP R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 190
    Processing helix  chain 'R' and resid 215 through 228
      removed outlier: 3.549A  pdb=" N   ILE R 221 " --> pdb=" O   GLN R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 253
      removed outlier: 3.644A  pdb=" N   ILE R 246 " --> pdb=" O   VAL R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 294
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 300 through 323
      removed outlier: 3.625A  pdb=" N   LEU R 306 " --> pdb=" O   LEU R 302 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
      removed outlier: 4.035A  pdb=" N   THR R 315 " --> pdb=" O   ALA R 311 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   ILE R 316 " --> pdb=" O   LYS R 312 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR R 317 " --> pdb=" O   SER R 313 " (cutoff:3.500A)
      Proline residue:  R 319  - end of helix
    Processing helix  chain 'R' and resid 326 through 335
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.581A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.524A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.605A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 352
      removed outlier: 3.570A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.704A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.715A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.632A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 52 through 56
      removed outlier: 3.626A  pdb=" N   SER S  55 " --> pdb=" O   SER S  52 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 52 through 56'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 194 through 197
      removed outlier: 3.625A  pdb=" N   HIS R 197 " --> pdb=" O   SER R 202 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   SER R 202 " --> pdb=" O   HIS R 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
      removed outlier: 6.692A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.593A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.613A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.782A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.613A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.586A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.805A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.478A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.783A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.619A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.747A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.747A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 141 through 142
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
    Processing sheet with id=AB7, first strand: chain 'S' and resid 155 through 157
      removed outlier: 3.503A  pdb=" N   VAL S 155 " --> pdb=" O   ILE S 216 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   THR S 213 " --> pdb=" O   SER S 206 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'S' and resid 177 through 178

    402 hydrogen bonds defined for protein.
    1158 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: 2.33

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2221
        1.33 -     1.45: 1926
        1.45 -     1.57: 4697
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 8940
  Sorted by residual:
  bond pdb=" N   LEU R 306 "
       pdb=" CA  LEU R 306 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 9.50e-03 1.11e+04 1.21e+01
  bond pdb=" N   VAL R 120 "
       pdb=" CA  VAL R 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.08e-02 8.57e+03 1.11e+01
  bond pdb=" N   ASN R 318 "
       pdb=" CA  ASN R 318 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.10e+01
  bond pdb=" N   GLY R 122 "
       pdb=" CA  GLY R 122 "
    ideal  model  delta    sigma   weight residual
    1.448  1.477 -0.028 8.80e-03 1.29e+04 1.04e+01
  bond pdb=" N   VAL A  34 "
       pdb=" CA  VAL A  34 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.12e-02 7.97e+03 9.49e+00
  ... (remaining 8935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 11559
        2.53 -     5.06: 544
        5.06 -     7.59: 40
        7.59 -    10.12: 7
       10.12 -    12.65: 3
  Bond angle restraints: 12153
  Sorted by residual:
  angle pdb=" N   PRO R 186 "
        pdb=" CA  PRO R 186 "
        pdb=" C   PRO R 186 "
      ideal   model   delta    sigma   weight residual
     110.70  119.15   -8.45 1.22e+00 6.72e-01 4.79e+01
  angle pdb=" CA  GLY R 122 "
        pdb=" C   GLY R 122 "
        pdb=" O   GLY R 122 "
      ideal   model   delta    sigma   weight residual
     122.37  118.10    4.27 7.30e-01 1.88e+00 3.43e+01
  angle pdb=" N   THR A 329 "
        pdb=" CA  THR A 329 "
        pdb=" C   THR A 329 "
      ideal   model   delta    sigma   weight residual
     113.02  106.70    6.32 1.20e+00 6.94e-01 2.78e+01
  angle pdb=" CA  ASP A 309 "
        pdb=" C   ASP A 309 "
        pdb=" O   ASP A 309 "
      ideal   model   delta    sigma   weight residual
     121.99  116.44    5.55 1.14e+00 7.69e-01 2.37e+01
  angle pdb=" CA  PRO R 186 "
        pdb=" C   PRO R 186 "
        pdb=" N   PRO R 187 "
      ideal   model   delta    sigma   weight residual
     117.93  123.41   -5.48 1.20e+00 6.94e-01 2.09e+01
  ... (remaining 12148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 4956
       17.23 -    34.45: 209
       34.45 -    51.68: 50
       51.68 -    68.91: 6
       68.91 -    86.14: 4
  Dihedral angle restraints: 5225
    sinusoidal: 1933
      harmonic: 3292
  Sorted by residual:
  dihedral pdb=" CA  ASP B 195 "
           pdb=" C   ASP B 195 "
           pdb=" N   THR B 196 "
           pdb=" CA  THR B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.47  -32.53     0      5.00e+00 4.00e-02 4.23e+01
  dihedral pdb=" CA  LEU A 353 "
           pdb=" C   LEU A 353 "
           pdb=" N   PHE A 354 "
           pdb=" CA  PHE A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.54   26.46     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.63   24.37     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 5222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 862
       0.061 -    0.123: 395
       0.123 -    0.184: 96
       0.184 -    0.245: 17
       0.245 -    0.307: 5
  Chirality restraints: 1375
  Sorted by residual:
  chirality pdb=" CG  LEU S 174 "
            pdb=" CB  LEU S 174 "
            pdb=" CD1 LEU S 174 "
            pdb=" CD2 LEU S 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" CA  VAL A  34 "
            pdb=" N   VAL A  34 "
            pdb=" C   VAL A  34 "
            pdb=" CB  VAL A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  TRP R 183 "
            pdb=" N   TRP R 183 "
            pdb=" C   TRP R 183 "
            pdb=" CB  TRP R 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1372 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "    0.024 2.00e-02 2.50e+03   2.02e-02 1.02e+01
        pdb=" CG  TRP S 111 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 234 "    0.023 2.00e-02 2.50e+03   2.41e-02 1.01e+01
        pdb=" CG  PHE B 234 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 234 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 234 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 234 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 234 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 278 "    0.015 2.00e-02 2.50e+03   2.08e-02 7.59e+00
        pdb=" CG  PHE B 278 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 278 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 278 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 278 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 278 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 278 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2674
        2.82 -     3.34: 7710
        3.34 -     3.86: 13965
        3.86 -     4.38: 15709
        4.38 -     4.90: 28188
  Nonbonded interactions: 68246
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   VAL R 104 "
            pdb=" OG  SER R 107 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG  SER A 293 "
            pdb=" OE1 GLU A 298 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.350 3.120
  ... (remaining 68241 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             43.740
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.330
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:   69.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
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      :  0.012   0.076   8940  Z= 0.795
  Angle     :  1.186  12.651  12153  Z= 0.759
  Chirality :  0.072   0.307   1375
  Planarity :  0.006   0.068   1532
  Dihedral  : 10.944  86.136   3102
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.60 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  3.27 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.77 (0.23), residues: 1121
  helix:  0.28 (0.24), residues: 390
  sheet: -3.37 (0.28), residues: 267
  loop : -2.67 (0.24), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP S 111 
 HIS   0.013   0.003   HIS S  35 
 PHE   0.055   0.004   PHE B 234 
 TYR   0.038   0.004   TYR S 227 
 ARG   0.009   0.001   ARG B 314 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 231
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   54 HIS cc_start: 0.8695 (m-70) cc_final: 0.8483 (m90)
REVERT: R  207 VAL cc_start: 0.8888 (t) cc_final: 0.8677 (m)
REVERT: A   24 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7108 (mtm-85)
REVERT: A  346 ASN cc_start: 0.8593 (m110) cc_final: 0.8236 (m110)
REVERT: B   44 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7257 (pm20)
REVERT: B   86 THR cc_start: 0.9245 (p) cc_final: 0.9000 (p)
REVERT: B  214 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7428 (mmt180)
REVERT: B  215 GLU cc_start: 0.8714 (mp0) cc_final: 0.8507 (mp0)
REVERT: B  295 ASN cc_start: 0.8850 (m-40) cc_final: 0.8633 (m-40)
REVERT: B  304 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8095 (ptm160)
REVERT: G   16 VAL cc_start: 0.8561 (p) cc_final: 0.8311 (m)
REVERT: G   17 GLU cc_start: 0.8692 (tp30) cc_final: 0.8474 (tp30)
REVERT: G   27 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8235 (mtt90)
REVERT: G   47 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8042 (mp0)
REVERT: S   65 LYS cc_start: 0.8539 (tttt) cc_final: 0.8103 (tttp)
REVERT: S   87 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7859 (mtm110)
REVERT: S  234 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7616 (pt0)
REVERT: S  244 LYS cc_start: 0.8170 (tttm) cc_final: 0.7802 (ttmm)
  outliers start: 15
  outliers final: 6
  residues processed: 244
  average time/residue: 0.2542
  time to fit residues: 81.4729
Evaluate side-chains
  164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  159 PHE
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  209 SER
Chi-restraints excluded: chain R residue  312 LYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
R 113 ASN
** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 129 GLN
R 331 ASN
B  44 GLN
B  91 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 268 ASN
B 340 ASN
G   5 ASN
S 194 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.093309 restraints weight = 13838.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.88
r_work: 0.3049 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8940  Z= 0.189
  Angle     :  0.603   8.400  12153  Z= 0.313
  Chirality :  0.043   0.156   1375
  Planarity :  0.004   0.056   1532
  Dihedral  :  7.041  80.330   1242
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 10.47 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.43 (0.25), residues: 1121
  helix:  1.86 (0.26), residues: 390
  sheet: -2.77 (0.29), residues: 257
  loop : -2.30 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 152 
 HIS   0.003   0.001   HIS S 232 
 PHE   0.014   0.002   PHE B 234 
 TYR   0.019   0.001   TYR R 194 
 ARG   0.005   0.001   ARG A  32 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 1.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   54 HIS cc_start: 0.8651 (m-70) cc_final: 0.8443 (m90)
REVERT: R  284 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7355 (t80)
REVERT: R  302 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7400 (mm)
REVERT: A   17 LYS cc_start: 0.8799 (mttt) cc_final: 0.8361 (mtpt)
REVERT: A   24 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7134 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8849 (t0) cc_final: 0.8383 (t0)
REVERT: A  332 VAL cc_start: 0.9110 (m) cc_final: 0.8772 (p)
REVERT: A  346 ASN cc_start: 0.8753 (m110) cc_final: 0.8418 (m110)
REVERT: B   42 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7239 (ttp80)
REVERT: B   44 GLN cc_start: 0.8021 (mm110) cc_final: 0.7428 (pm20)
REVERT: B  156 GLN cc_start: 0.8214 (mt0) cc_final: 0.7760 (mt0)
REVERT: B  215 GLU cc_start: 0.8785 (mp0) cc_final: 0.8456 (mp0)
REVERT: G   17 GLU cc_start: 0.8656 (tp30) cc_final: 0.8440 (tp30)
REVERT: G   27 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8183 (mtt90)
REVERT: G   47 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8256 (mp0)
REVERT: S   65 LYS cc_start: 0.8568 (tttt) cc_final: 0.8096 (tttp)
REVERT: S   87 ARG cc_start: 0.8119 (ptp-170) cc_final: 0.7870 (mtm110)
REVERT: S  234 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7811 (pt0)
REVERT: S  244 LYS cc_start: 0.8320 (tttm) cc_final: 0.7916 (ttmm)
  outliers start: 24
  outliers final: 16
  residues processed: 204
  average time/residue: 0.2986
  time to fit residues: 81.5442
Evaluate side-chains
  168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 ILE
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  284 TYR
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0670
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B  75 GLN
B 220 GLN
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.092228 restraints weight = 14096.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.82
r_work: 0.3046 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8940  Z= 0.205
  Angle     :  0.566   8.548  12153  Z= 0.292
  Chirality :  0.042   0.144   1375
  Planarity :  0.004   0.050   1532
  Dihedral  :  6.356  80.332   1234
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 12.98 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.07 (0.25), residues: 1121
  helix:  2.23 (0.26), residues: 389
  sheet: -2.59 (0.28), residues: 269
  loop : -2.12 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R  51 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.016   0.002   PHE S  68 
 TYR   0.022   0.001   TYR R 118 
 ARG   0.005   0.000   ARG B 251 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   45 TYR cc_start: 0.7885 (m-80) cc_final: 0.7581 (m-80)
REVERT: R  152 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.8233 (t60)
REVERT: R  220 MET cc_start: 0.8889 (tpp) cc_final: 0.8681 (tpp)
REVERT: R  302 LEU cc_start: 0.7809 (pt) cc_final: 0.7462 (mm)
REVERT: A   17 LYS cc_start: 0.8775 (mttt) cc_final: 0.8323 (mtpt)
REVERT: A   24 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7063 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8870 (t0) cc_final: 0.8382 (t0)
REVERT: A  332 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8789 (p)
REVERT: B   42 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7399 (ttp80)
REVERT: B  161 SER cc_start: 0.9350 (t) cc_final: 0.8674 (p)
REVERT: G   27 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8142 (mtt90)
REVERT: G   47 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8208 (mp0)
REVERT: S   65 LYS cc_start: 0.8626 (tttt) cc_final: 0.8128 (tttp)
REVERT: S  186 GLN cc_start: 0.7913 (mt0) cc_final: 0.7628 (mt0)
REVERT: S  234 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7858 (pt0)
REVERT: S  244 LYS cc_start: 0.8327 (tttm) cc_final: 0.7902 (ttmm)
  outliers start: 32
  outliers final: 20
  residues processed: 183
  average time/residue: 0.2375
  time to fit residues: 57.7605
Evaluate side-chains
  169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 ILE
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  152 TRP
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0070
   chunk 73 optimal weight:    0.8980
   chunk 59 optimal weight:    0.2980
   chunk 85 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
R  94 ASN
** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.129500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.095121 restraints weight = 13821.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.77
r_work: 0.3086 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8940  Z= 0.154
  Angle     :  0.533   9.694  12153  Z= 0.274
  Chirality :  0.041   0.165   1375
  Planarity :  0.004   0.044   1532
  Dihedral  :  5.951  76.750   1234
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.29 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.75 (0.26), residues: 1121
  helix:  2.46 (0.27), residues: 389
  sheet: -2.41 (0.27), residues: 278
  loop : -1.87 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP R  51 
 HIS   0.002   0.001   HIS S 232 
 PHE   0.014   0.001   PHE S  68 
 TYR   0.024   0.001   TYR R 118 
 ARG   0.005   0.000   ARG S 218 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   54 HIS cc_start: 0.8606 (m90) cc_final: 0.8366 (m90)
REVERT: R  152 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7607 (t-100)
REVERT: R  302 LEU cc_start: 0.7757 (pt) cc_final: 0.7387 (mm)
REVERT: R  331 ASN cc_start: 0.8009 (p0) cc_final: 0.7568 (p0)
REVERT: A   17 LYS cc_start: 0.8663 (mttt) cc_final: 0.8221 (mtpt)
REVERT: A   24 ARG cc_start: 0.7455 (mtm110) cc_final: 0.6981 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8832 (t0) cc_final: 0.8379 (t0)
REVERT: A  332 VAL cc_start: 0.9145 (m) cc_final: 0.8812 (p)
REVERT: A  341 ASP cc_start: 0.8507 (t0) cc_final: 0.8301 (t0)
REVERT: B   42 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7382 (ttp80)
REVERT: B  161 SER cc_start: 0.9278 (t) cc_final: 0.8608 (p)
REVERT: G   27 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8284 (mtt90)
REVERT: G   42 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: G   47 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8193 (mp0)
REVERT: S   65 LYS cc_start: 0.8643 (tttt) cc_final: 0.8138 (tttp)
REVERT: S   95 TYR cc_start: 0.8629 (m-80) cc_final: 0.7608 (m-80)
REVERT: S  160 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7108 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7828 (pt0)
REVERT: S  244 LYS cc_start: 0.8306 (tttm) cc_final: 0.7879 (ttmm)
  outliers start: 29
  outliers final: 20
  residues processed: 194
  average time/residue: 0.2267
  time to fit residues: 59.2792
Evaluate side-chains
  182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  152 TRP
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  249 VAL
Chi-restraints excluded: chain R residue  273 MET
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    0.0010
   chunk 106 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.1792

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

Flipped N/Q/H residues before XYZ refinement:
** R 114 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 = 0.3663 r_free = 0.3663 target = 0.127552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.092277 restraints weight = 14038.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.83
r_work: 0.3042 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8940  Z= 0.204
  Angle     :  0.540  10.064  12153  Z= 0.277
  Chirality :  0.041   0.137   1375
  Planarity :  0.004   0.045   1532
  Dihedral  :  5.908  81.142   1234
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.16 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.71 (0.26), residues: 1121
  helix:  2.41 (0.27), residues: 389
  sheet: -2.35 (0.27), residues: 285
  loop : -1.77 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP R  51 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.013   0.001   PHE S  68 
 TYR   0.022   0.001   TYR R 118 
 ARG   0.003   0.000   ARG B 251 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   54 HIS cc_start: 0.8668 (m90) cc_final: 0.8354 (m90)
REVERT: R  152 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.8242 (t60)
REVERT: R  217 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8156 (tp40)
REVERT: R  302 LEU cc_start: 0.7669 (pt) cc_final: 0.7310 (mm)
REVERT: R  331 ASN cc_start: 0.7944 (p0) cc_final: 0.7521 (p0)
REVERT: A    8 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7402 (mt-10)
REVERT: A   17 LYS cc_start: 0.8760 (mttt) cc_final: 0.8316 (mtpt)
REVERT: A   24 ARG cc_start: 0.7541 (mtm110) cc_final: 0.7062 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8849 (t0) cc_final: 0.8426 (t0)
REVERT: A  332 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8794 (p)
REVERT: B   42 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7197 (ttp80)
REVERT: B   44 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7524 (pm20)
REVERT: B  161 SER cc_start: 0.9316 (t) cc_final: 0.8634 (p)
REVERT: B  301 LYS cc_start: 0.8628 (ptpt) cc_final: 0.8378 (mtpp)
REVERT: G   27 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8323 (mtt90)
REVERT: G   47 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8229 (mp0)
REVERT: S   65 LYS cc_start: 0.8641 (tttt) cc_final: 0.8159 (tttp)
REVERT: S   87 ARG cc_start: 0.8405 (mtm110) cc_final: 0.7930 (ptp-110)
REVERT: S  160 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7166 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7912 (pt0)
REVERT: S  244 LYS cc_start: 0.8415 (tttm) cc_final: 0.7979 (ttmm)
  outliers start: 32
  outliers final: 23
  residues processed: 185
  average time/residue: 0.2247
  time to fit residues: 55.5054
Evaluate side-chains
  177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  152 TRP
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  273 MET
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** R 114 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 = 0.3654 r_free = 0.3654 target = 0.126983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.091444 restraints weight = 14065.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.83
r_work: 0.3032 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8940  Z= 0.219
  Angle     :  0.549  10.285  12153  Z= 0.280
  Chirality :  0.041   0.149   1375
  Planarity :  0.004   0.046   1532
  Dihedral  :  5.897  83.119   1234
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.38 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.61 (0.26), residues: 1121
  helix:  2.46 (0.27), residues: 388
  sheet: -2.28 (0.27), residues: 283
  loop : -1.68 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R  51 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.015   0.001   PHE S  68 
 TYR   0.022   0.001   TYR R 118 
 ARG   0.002   0.000   ARG S 180 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   54 HIS cc_start: 0.8679 (m90) cc_final: 0.8344 (m90)
REVERT: R  220 MET cc_start: 0.8794 (tpp) cc_final: 0.8511 (tpt)
REVERT: R  302 LEU cc_start: 0.7731 (pt) cc_final: 0.7362 (mm)
REVERT: R  331 ASN cc_start: 0.7982 (p0) cc_final: 0.7579 (p0)
REVERT: A    8 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7398 (mt-10)
REVERT: A   17 LYS cc_start: 0.8773 (mttt) cc_final: 0.8366 (mtpt)
REVERT: A   24 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7083 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8852 (t0) cc_final: 0.8460 (t0)
REVERT: B   42 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7173 (ttp80)
REVERT: B   44 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7552 (pm20)
REVERT: B  161 SER cc_start: 0.9326 (t) cc_final: 0.8651 (p)
REVERT: B  262 MET cc_start: 0.8502 (mpp) cc_final: 0.8010 (mpp)
REVERT: G   27 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8321 (mtt90)
REVERT: G   47 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8205 (mp0)
REVERT: S   65 LYS cc_start: 0.8703 (tttt) cc_final: 0.8227 (tttp)
REVERT: S   87 ARG cc_start: 0.8359 (mtm110) cc_final: 0.7926 (ptp-110)
REVERT: S   98 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8673 (ptt-90)
REVERT: S  160 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7216 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7938 (pt0)
REVERT: S  244 LYS cc_start: 0.8383 (tttm) cc_final: 0.7947 (ttmm)
  outliers start: 35
  outliers final: 26
  residues processed: 180
  average time/residue: 0.2293
  time to fit residues: 55.3858
Evaluate side-chains
  175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  273 MET
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain R residue  334 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0470
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.128941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.093519 restraints weight = 14089.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.84
r_work: 0.3057 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8940  Z= 0.154
  Angle     :  0.529  11.765  12153  Z= 0.268
  Chirality :  0.040   0.150   1375
  Planarity :  0.004   0.044   1532
  Dihedral  :  5.765  85.604   1234
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.49 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.40 (0.26), residues: 1121
  helix:  2.55 (0.27), residues: 387
  sheet: -2.08 (0.28), residues: 285
  loop : -1.54 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R  51 
 HIS   0.002   0.001   HIS R  54 
 PHE   0.018   0.001   PHE R 208 
 TYR   0.023   0.001   TYR R 118 
 ARG   0.004   0.000   ARG S 218 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   50 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7690 (mmm160)
REVERT: R   54 HIS cc_start: 0.8618 (m90) cc_final: 0.8328 (m-70)
REVERT: R  302 LEU cc_start: 0.7699 (pt) cc_final: 0.7355 (mm)
REVERT: R  331 ASN cc_start: 0.7963 (p0) cc_final: 0.7563 (p0)
REVERT: A    8 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7338 (mt-10)
REVERT: A   17 LYS cc_start: 0.8713 (mttt) cc_final: 0.8304 (mtpt)
REVERT: A   24 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7084 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8853 (t0) cc_final: 0.8491 (t0)
REVERT: B   42 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7172 (ttp80)
REVERT: B   44 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7561 (pm20)
REVERT: B  161 SER cc_start: 0.9258 (t) cc_final: 0.8616 (p)
REVERT: B  262 MET cc_start: 0.8438 (mpp) cc_final: 0.7985 (mpp)
REVERT: G   27 ARG cc_start: 0.8603 (mtt90) cc_final: 0.8317 (mtt90)
REVERT: G   47 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8216 (mp0)
REVERT: S   65 LYS cc_start: 0.8713 (tttt) cc_final: 0.8236 (tttp)
REVERT: S   87 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7922 (ptp-110)
REVERT: S   98 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8592 (ptt-90)
REVERT: S  160 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7198 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7918 (pt0)
REVERT: S  244 LYS cc_start: 0.8398 (tttm) cc_final: 0.7957 (ttmm)
  outliers start: 34
  outliers final: 26
  residues processed: 182
  average time/residue: 0.2161
  time to fit residues: 53.2610
Evaluate side-chains
  179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue   50 ARG
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  273 MET
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   86 LEU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.1980
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    0.5980
   chunk 82 optimal weight:    0.1980
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  88 ASN
B 183 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.130468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.095496 restraints weight = 14244.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.06
r_work: 0.3075 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8940  Z= 0.137
  Angle     :  0.525  13.716  12153  Z= 0.262
  Chirality :  0.040   0.149   1375
  Planarity :  0.003   0.044   1532
  Dihedral  :  5.691  89.464   1234
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.68 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.16 (0.26), residues: 1121
  helix:  2.67 (0.27), residues: 386
  sheet: -1.82 (0.29), residues: 277
  loop : -1.41 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R  51 
 HIS   0.002   0.000   HIS R 197 
 PHE   0.012   0.001   PHE S  68 
 TYR   0.023   0.001   TYR R 118 
 ARG   0.003   0.000   ARG B  46 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 1.739 
Fit side-chains
   revert: symmetry clash
REVERT: R   50 ARG cc_start: 0.8001 (mpp80) cc_final: 0.7693 (tpp80)
REVERT: R   54 HIS cc_start: 0.8660 (m90) cc_final: 0.8356 (m-70)
REVERT: R  200 LYS cc_start: 0.8405 (mttt) cc_final: 0.7977 (mmtt)
REVERT: R  302 LEU cc_start: 0.7674 (pt) cc_final: 0.7287 (mm)
REVERT: R  331 ASN cc_start: 0.7960 (p0) cc_final: 0.7568 (p0)
REVERT: A    8 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7292 (mt-10)
REVERT: A   17 LYS cc_start: 0.8658 (mttt) cc_final: 0.8256 (mtpt)
REVERT: A   24 ARG cc_start: 0.7517 (mtm110) cc_final: 0.7087 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8844 (t0) cc_final: 0.8499 (t0)
REVERT: B   42 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7182 (ttp80)
REVERT: B   44 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7549 (pm20)
REVERT: B  161 SER cc_start: 0.9189 (t) cc_final: 0.8556 (p)
REVERT: B  215 GLU cc_start: 0.8718 (mp0) cc_final: 0.8425 (mp0)
REVERT: B  262 MET cc_start: 0.8431 (mpp) cc_final: 0.8025 (mpp)
REVERT: G   27 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8342 (mtt90)
REVERT: G   47 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8126 (mp0)
REVERT: S   65 LYS cc_start: 0.8729 (tttt) cc_final: 0.8258 (tttp)
REVERT: S   87 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7916 (ptp-110)
REVERT: S   98 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8570 (ptt-90)
REVERT: S  160 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7207 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7892 (pt0)
REVERT: S  244 LYS cc_start: 0.8358 (tttm) cc_final: 0.7913 (ttmm)
  outliers start: 26
  outliers final: 22
  residues processed: 173
  average time/residue: 0.2706
  time to fit residues: 63.1828
Evaluate side-chains
  169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    0.0870
   chunk 82 optimal weight:    0.0040
   chunk 97 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.4970

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.130800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.094971 restraints weight = 14137.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.88
r_work: 0.3081 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8940  Z= 0.146
  Angle     :  0.522  13.855  12153  Z= 0.261
  Chirality :  0.040   0.169   1375
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.593  87.329   1234
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.12 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.26), residues: 1121
  helix:  2.70 (0.27), residues: 387
  sheet: -1.73 (0.29), residues: 277
  loop : -1.32 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  51 
 HIS   0.002   0.000   HIS B 142 
 PHE   0.046   0.001   PHE R 208 
 TYR   0.025   0.001   TYR R 118 
 ARG   0.002   0.000   ARG S 218 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
REVERT: R   50 ARG cc_start: 0.8042 (mpp80) cc_final: 0.7817 (mmm160)
REVERT: R   54 HIS cc_start: 0.8669 (m90) cc_final: 0.8400 (m-70)
REVERT: R   73 LEU cc_start: 0.8857 (mt) cc_final: 0.8569 (mp)
REVERT: R  200 LYS cc_start: 0.8423 (mttt) cc_final: 0.7981 (mmtt)
REVERT: R  302 LEU cc_start: 0.7632 (pt) cc_final: 0.7304 (mm)
REVERT: R  331 ASN cc_start: 0.7944 (p0) cc_final: 0.7558 (p0)
REVERT: A    8 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7308 (mt-10)
REVERT: A   17 LYS cc_start: 0.8637 (mttt) cc_final: 0.8243 (mtpt)
REVERT: A   24 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7078 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8832 (t0) cc_final: 0.8503 (t0)
REVERT: B   42 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7138 (ttp80)
REVERT: B   44 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7538 (pm20)
REVERT: B  161 SER cc_start: 0.9185 (t) cc_final: 0.8563 (p)
REVERT: B  215 GLU cc_start: 0.8702 (mp0) cc_final: 0.8396 (mp0)
REVERT: B  262 MET cc_start: 0.8405 (mpp) cc_final: 0.8049 (mpp)
REVERT: G   27 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8362 (mtt90)
REVERT: G   47 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8107 (mp0)
REVERT: S   18 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7329 (ttm170)
REVERT: S   65 LYS cc_start: 0.8802 (tttt) cc_final: 0.8324 (tttp)
REVERT: S   87 ARG cc_start: 0.8286 (mtm110) cc_final: 0.7896 (ptp-110)
REVERT: S   98 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8590 (ptt-90)
REVERT: S  160 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7211 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7876 (pt0)
REVERT: S  244 LYS cc_start: 0.8359 (tttm) cc_final: 0.7902 (ttmm)
  outliers start: 28
  outliers final: 24
  residues processed: 172
  average time/residue: 0.2714
  time to fit residues: 61.8458
Evaluate side-chains
  171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0000
   chunk 84 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0980
   chunk 109 optimal weight:    0.9990
   chunk 95 optimal weight:    0.1980
   overall best weight:    0.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.096466 restraints weight = 14031.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.86
r_work: 0.3106 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8940  Z= 0.133
  Angle     :  0.526  13.909  12153  Z= 0.261
  Chirality :  0.040   0.171   1375
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.496  85.743   1234
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.67 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.04 (0.26), residues: 1121
  helix:  2.72 (0.27), residues: 388
  sheet: -1.59 (0.29), residues: 277
  loop : -1.28 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.001   TRP R  51 
 HIS   0.001   0.000   HIS R  46 
 PHE   0.011   0.001   PHE S  68 
 TYR   0.024   0.001   TYR R 118 
 ARG   0.002   0.000   ARG S 180 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   50 ARG cc_start: 0.8175 (mpp80) cc_final: 0.7844 (mmm160)
REVERT: R   51 TRP cc_start: 0.8199 (p90) cc_final: 0.7670 (p90)
REVERT: R   54 HIS cc_start: 0.8675 (m90) cc_final: 0.8427 (m-70)
REVERT: R   73 LEU cc_start: 0.8858 (mt) cc_final: 0.8580 (mp)
REVERT: R  200 LYS cc_start: 0.8454 (mttt) cc_final: 0.8001 (mmtt)
REVERT: R  302 LEU cc_start: 0.7615 (pt) cc_final: 0.7223 (mm)
REVERT: R  325 MET cc_start: 0.8058 (mmt) cc_final: 0.7840 (mmm)
REVERT: R  331 ASN cc_start: 0.7913 (p0) cc_final: 0.7524 (p0)
REVERT: A    8 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7266 (mt-10)
REVERT: A   17 LYS cc_start: 0.8598 (mttt) cc_final: 0.8252 (mtpt)
REVERT: A   24 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7071 (mtm-85)
REVERT: A  256 ASN cc_start: 0.8805 (t0) cc_final: 0.8495 (t0)
REVERT: B   42 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7193 (ttp80)
REVERT: B   44 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7557 (pm20)
REVERT: B  161 SER cc_start: 0.9073 (t) cc_final: 0.8490 (p)
REVERT: B  215 GLU cc_start: 0.8686 (mp0) cc_final: 0.8371 (mp0)
REVERT: B  262 MET cc_start: 0.8372 (mpp) cc_final: 0.8044 (mpp)
REVERT: G   27 ARG cc_start: 0.8649 (mtt90) cc_final: 0.8366 (mtt90)
REVERT: G   47 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7995 (mp0)
REVERT: S   18 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7386 (ttm170)
REVERT: S   65 LYS cc_start: 0.8799 (tttt) cc_final: 0.8327 (tttp)
REVERT: S   87 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7862 (ptp-110)
REVERT: S   98 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8500 (ptt-90)
REVERT: S  160 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7210 (mmm-85)
REVERT: S  234 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7849 (pt0)
REVERT: S  244 LYS cc_start: 0.8370 (tttm) cc_final: 0.7907 (ttmm)
  outliers start: 25
  outliers final: 21
  residues processed: 177
  average time/residue: 0.2466
  time to fit residues: 57.9311
Evaluate side-chains
  179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 ILE
Chi-restraints excluded: chain R residue  148 SER
Chi-restraints excluded: chain R residue  179 TRP
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  265 GLU
Chi-restraints excluded: chain R residue  294 ASN
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 77 optimal weight:    0.2980
   chunk 79 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.129733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.094110 restraints weight = 14031.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.85
r_work: 0.3067 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8940  Z= 0.184
  Angle     :  0.558  13.485  12153  Z= 0.274
  Chirality :  0.041   0.260   1375
  Planarity :  0.004   0.044   1532
  Dihedral  :  5.541  84.988   1234
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.56 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.07 (0.26), residues: 1121
  helix:  2.74 (0.27), residues: 386
  sheet: -1.58 (0.29), residues: 277
  loop : -1.24 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.001   TRP R  51 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.016   0.001   PHE S  68 
 TYR   0.029   0.001   TYR R 118 
 ARG   0.002   0.000   ARG B 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4823.55 seconds
wall clock time: 85 minutes 50.73 seconds (5150.73 seconds total)