Starting phenix.real_space_refine
on Tue Jul 29 00:27:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rbt_24401/07_2025/7rbt_24401_neut.cif"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    6915      2.51       5
     N    1903      2.21       5
     O    1999      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10881
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1792
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 6, 'TRANS': 213}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2581
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "E"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1748
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 969
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "P"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 246
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'AIB:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "R"
      Number of atoms: 3072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 3072
          Classifications: {'peptide': 378}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 14, 'TRANS': 363}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'41Y': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.99, per 1000 atoms: 0.64
  Number of scatterers: 10881
  At special positions: 0
  Unit cell: (167.232, 124.8, 104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     F       1      9.00
     O    1999      8.00
     N    1903      7.00
     C    6915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  70 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  61 " - pdb=" SG  CYS R 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  84 " - pdb=" SG  CYS R 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 216 " - pdb=" SG  CYS R 286 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2570

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 19 sheets defined
      34.4% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 3.882A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 59
      removed outlier: 3.587A  pdb=" N   LYS A  58 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.560A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.834A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.604A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.662A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.519A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 4.183A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 56
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 43
      removed outlier: 3.596A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.616A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
    Processing helix  chain 'R' and resid 31 through 53
    Processing helix  chain 'R' and resid 126 through 162
      removed outlier: 4.002A  pdb=" N   LEU R 161 " --> pdb=" O   LEU R 157 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   PHE R 162 " --> pdb=" O   ILE R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 193
    Processing helix  chain 'R' and resid 209 through 247
    Processing helix  chain 'R' and resid 252 through 281
      Proline residue:  R 267  - end of helix
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 293 through 327
      removed outlier: 4.811A  pdb=" N   ILE R 299 " --> pdb=" O   ILE R 295 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 336 through 347
    Processing helix  chain 'R' and resid 348 through 351
    Processing helix  chain 'R' and resid 362 through 366
      removed outlier: 3.738A  pdb=" N   ARG R 366 " --> pdb=" O   GLU R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 373
    Processing helix  chain 'R' and resid 373 through 392
      removed outlier: 5.379A  pdb=" N   GLY R 385 " --> pdb=" O   SER R 381 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   PHE R 386 " --> pdb=" O   SER R 382 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 396 through 410
      removed outlier: 3.684A  pdb=" N   CYS R 410 " --> pdb=" O   GLY R 406 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45
      removed outlier: 6.469A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249
      removed outlier: 3.744A  pdb=" N   LEU A 289 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.633A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.752A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.534A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 149
      removed outlier: 3.996A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.829A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.145A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277
      removed outlier: 3.512A  pdb=" N   VAL B 296 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.721A  pdb=" N   LEU E  20 " --> pdb=" O   LEU E  81 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.688A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.457A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 183
      removed outlier: 6.433A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL E 214 " --> pdb=" O   GLN E 167 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 193 through 196
    Processing sheet with id=AB7, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.517A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.728A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'R' and resid 64 through 65
      removed outlier: 3.508A  pdb=" N   SER R  64 " --> pdb=" O   TRP R  71 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TRP R  71 " --> pdb=" O   SER R  64 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'R' and resid 78 through 80
      removed outlier: 4.037A  pdb=" N   ALA R  78 " --> pdb=" O   CYS R 103 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG R 101 " --> pdb=" O   ALA R  80 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1362 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: 3.78

  Time building geometry restraints manager: 3.10 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: 3092
        1.33 -     1.46: 2759
        1.46 -     1.58: 5183
        1.58 -     1.71: 3
        1.71 -     1.83: 87
  Bond restraints: 11124
  Sorted by residual:
  bond pdb=" C11 41Y R 501 "
       pdb=" N10 41Y R 501 "
    ideal  model  delta    sigma   weight residual
    1.476  1.341  0.135 2.00e-02 2.50e+03 4.53e+01
  bond pdb=" C24 41Y R 501 "
       pdb=" C25 41Y R 501 "
    ideal  model  delta    sigma   weight residual
    1.486  1.384  0.102 2.00e-02 2.50e+03 2.59e+01
  bond pdb=" C06 41Y R 501 "
       pdb=" C07 41Y R 501 "
    ideal  model  delta    sigma   weight residual
    1.398  1.312  0.086 2.00e-02 2.50e+03 1.86e+01
  bond pdb=" C22 41Y R 501 "
       pdb=" N10 41Y R 501 "
    ideal  model  delta    sigma   weight residual
    1.473  1.393  0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" C08 41Y R 501 "
       pdb=" C09 41Y R 501 "
    ideal  model  delta    sigma   weight residual
    1.526  1.593 -0.067 2.00e-02 2.50e+03 1.12e+01
  ... (remaining 11119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 14635
        1.90 -     3.80: 404
        3.80 -     5.69: 51
        5.69 -     7.59: 6
        7.59 -     9.49: 2
  Bond angle restraints: 15098
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     112.23  104.49    7.74 1.26e+00 6.30e-01 3.77e+01
  angle pdb=" CA  ASP B  76 "
        pdb=" CB  ASP B  76 "
        pdb=" CG  ASP B  76 "
      ideal   model   delta    sigma   weight residual
     112.60  117.65   -5.05 1.00e+00 1.00e+00 2.55e+01
  angle pdb=" N   AIB P   2 "
        pdb=" CA  AIB P   2 "
        pdb=" C   AIB P   2 "
      ideal   model   delta    sigma   weight residual
     111.00  120.49   -9.49 2.80e+00 1.28e-01 1.15e+01
  angle pdb=" N   ASP B 298 "
        pdb=" CA  ASP B 298 "
        pdb=" C   ASP B 298 "
      ideal   model   delta    sigma   weight residual
     110.30  105.54    4.76 1.50e+00 4.44e-01 1.01e+01
  angle pdb=" N   VAL N 110 "
        pdb=" CA  VAL N 110 "
        pdb=" C   VAL N 110 "
      ideal   model   delta    sigma   weight residual
     113.07  108.89    4.18 1.37e+00 5.33e-01 9.31e+00
  ... (remaining 15093 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 5888
       17.58 -    35.16: 535
       35.16 -    52.74: 115
       52.74 -    70.32: 23
       70.32 -    87.89: 13
  Dihedral angle restraints: 6574
    sinusoidal: 2575
      harmonic: 3999
  Sorted by residual:
  dihedral pdb=" CA  THR E 160 "
           pdb=" C   THR E 160 "
           pdb=" N   TYR E 161 "
           pdb=" CA  TYR E 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.37  -24.63     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  CYS R 167 "
           pdb=" C   CYS R 167 "
           pdb=" N   THR R 168 "
           pdb=" CA  THR R 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  TRP B  63 "
           pdb=" C   TRP B  63 "
           pdb=" N   GLY B  64 "
           pdb=" CA  GLY B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.21   19.79     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 6571 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1068
       0.038 -    0.077: 431
       0.077 -    0.115: 136
       0.115 -    0.153: 33
       0.153 -    0.191: 5
  Chirality restraints: 1673
  Sorted by residual:
  chirality pdb=" CA  ASP B  76 "
            pdb=" N   ASP B  76 "
            pdb=" C   ASP B  76 "
            pdb=" CB  ASP B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" CA  ASP B 298 "
            pdb=" N   ASP B 298 "
            pdb=" C   ASP B 298 "
            pdb=" CB  ASP B 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CA  TYR R 259 "
            pdb=" N   TYR R 259 "
            pdb=" C   TYR R 259 "
            pdb=" CB  TYR R 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.66e-01
  ... (remaining 1670 not shown)

  Planarity restraints: 1921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY P   4 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.16e+00
        pdb=" C   GLY P   4 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY P   4 "    0.020 2.00e-02 2.50e+03
        pdb=" N   THR P   5 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 371 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   PHE R 371 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE R 371 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ALA R 372 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 141 "   -0.016 2.00e-02 2.50e+03   1.66e-02 5.51e+00
        pdb=" CG  TYR R 141 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 141 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 141 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 141 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 141 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR R 141 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1918 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 237
        2.65 -     3.22: 11243
        3.22 -     3.78: 16638
        3.78 -     4.34: 24110
        4.34 -     4.90: 38477
  Nonbonded interactions: 90705
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" NH1 ARG R 190 "
            pdb=" OD1 ASP R 191 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" O   THR B 274 "
            pdb=" OG  SER B 275 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" NE2 GLN E  82 "
            pdb=" O   MET E  83 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.218 3.040
  ... (remaining 90700 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:             2.710
  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:          0.480
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.370
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
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      :  0.007   0.135  11132  Z= 0.309
  Angle     :  0.763   9.489  15114  Z= 0.421
  Chirality :  0.046   0.191   1673
  Planarity :  0.005   0.053   1921
  Dihedral  : 14.773  87.894   3980
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  1.75 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -2.82 (0.21), residues: 1353
  helix: -0.63 (0.23), residues: 421
  sheet: -2.34 (0.26), residues: 342
  loop : -2.42 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP P  25 
 HIS   0.010   0.002   HIS R 166 
 PHE   0.030   0.002   PHE R 270 
 TYR   0.041   0.003   TYR R 141 
 ARG   0.018   0.001   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19257 (  484)
  hydrogen bonds       : angle       7.88753 ( 1362)
  SS BOND              : bond        0.00507 (    8)
  SS BOND              : angle       1.90347 (   16)
  covalent geometry    : bond        0.00681 (11124)
  covalent geometry    : angle       0.76096 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 195
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7048 (mtp-110) cc_final: 0.6483 (mtp85)
REVERT: B   23 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7374 (ttmt)
REVERT: B   76 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (p0)
REVERT: R  109 TRP cc_start: 0.2406 (m100) cc_final: 0.2028 (m100)
REVERT: R  199 PRO cc_start: 0.6800 (Cg_endo) cc_final: 0.6509 (Cg_exo)
REVERT: R  204 GLN cc_start: 0.4612 (tp40) cc_final: 0.4350 (tp40)
REVERT: R  287 TRP cc_start: 0.6442 (m-10) cc_final: 0.5939 (m-10)
REVERT: R  395 ILE cc_start: 0.7583 (mm) cc_final: 0.7331 (mm)
  outliers start: 8
  outliers final: 2
  residues processed: 201
  average time/residue: 0.2618
  time to fit residues: 72.3059
Evaluate side-chains
  167 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 102 optimal weight:    0.4980
   chunk 56 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
R  93 HIS
R 117 GLN
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 230 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.166632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.136007 restraints weight = 15821.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.22
r_work: 0.3756 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11132  Z= 0.161
  Angle     :  0.715  11.284  15114  Z= 0.367
  Chirality :  0.046   0.182   1673
  Planarity :  0.005   0.049   1921
  Dihedral  :  6.026  59.322   1563
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  8.73 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.90 (0.22), residues: 1353
  helix:  0.06 (0.24), residues: 432
  sheet: -1.83 (0.27), residues: 320
  loop : -1.85 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP P  25 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.024   0.002   PHE R 270 
 TYR   0.025   0.002   TYR R 259 
 ARG   0.007   0.001   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05011 (  484)
  hydrogen bonds       : angle       5.73307 ( 1362)
  SS BOND              : bond        0.00370 (    8)
  SS BOND              : angle       1.36084 (   16)
  covalent geometry    : bond        0.00357 (11124)
  covalent geometry    : angle       0.71398 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6467 (mtp85)
REVERT: B   23 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7556 (ttmt)
REVERT: B  211 TRP cc_start: 0.8205 (m100) cc_final: 0.7873 (m100)
REVERT: B  336 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: E    3 GLN cc_start: 0.6684 (tm-30) cc_final: 0.6427 (tm-30)
REVERT: E   90 ASP cc_start: 0.6753 (m-30) cc_final: 0.6508 (m-30)
REVERT: E  148 ARG cc_start: 0.6260 (mmp80) cc_final: 0.5953 (mmt90)
REVERT: E  215 TYR cc_start: 0.8112 (m-10) cc_final: 0.7865 (m-80)
REVERT: P    7 THR cc_start: 0.7706 (m) cc_final: 0.7433 (p)
REVERT: R   37 GLN cc_start: 0.7079 (mm110) cc_final: 0.6134 (tm-30)
REVERT: R  109 TRP cc_start: 0.2236 (m100) cc_final: 0.1664 (m100)
REVERT: R  140 MET cc_start: 0.7474 (tmm) cc_final: 0.7225 (tmm)
REVERT: R  182 LEU cc_start: 0.7069 (tp) cc_final: 0.6704 (tp)
REVERT: R  199 PRO cc_start: 0.6709 (Cg_endo) cc_final: 0.6441 (Cg_exo)
REVERT: R  204 GLN cc_start: 0.4490 (tp40) cc_final: 0.4259 (tp40)
REVERT: R  287 TRP cc_start: 0.6397 (m-10) cc_final: 0.5102 (m-10)
REVERT: R  395 ILE cc_start: 0.7973 (mm) cc_final: 0.7640 (mm)
  outliers start: 31
  outliers final: 17
  residues processed: 221
  average time/residue: 0.3079
  time to fit residues: 90.9797
Evaluate side-chains
  181 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 1.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  363 GLU
Chi-restraints excluded: chain R residue  407 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 132 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   1 GLN
N  39 GLN
P  19 GLN
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.163325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.132488 restraints weight = 16381.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.36
r_work: 0.3683 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11132  Z= 0.240
  Angle     :  0.763  11.775  15114  Z= 0.388
  Chirality :  0.047   0.188   1673
  Planarity :  0.005   0.046   1921
  Dihedral  :  6.050  58.161   1561
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 13.62 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.85 (0.22), residues: 1353
  helix:  0.05 (0.24), residues: 428
  sheet: -1.65 (0.28), residues: 322
  loop : -1.86 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 233 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.026   0.002   PHE R 270 
 TYR   0.031   0.003   TYR R 259 
 ARG   0.007   0.001   ARG N  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  484)
  hydrogen bonds       : angle       5.68537 ( 1362)
  SS BOND              : bond        0.00473 (    8)
  SS BOND              : angle       1.33647 (   16)
  covalent geometry    : bond        0.00559 (11124)
  covalent geometry    : angle       0.76184 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 GLU cc_start: 0.3301 (OUTLIER) cc_final: 0.2819 (pp20)
REVERT: B   19 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6580 (mtp85)
REVERT: B   23 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7538 (ttmt)
REVERT: B  211 TRP cc_start: 0.8243 (m100) cc_final: 0.7979 (m100)
REVERT: E  161 TYR cc_start: 0.8396 (m-80) cc_final: 0.8116 (m-80)
REVERT: R   37 GLN cc_start: 0.7199 (mm110) cc_final: 0.6263 (tm-30)
REVERT: R  109 TRP cc_start: 0.2033 (m100) cc_final: 0.1479 (m100)
REVERT: R  125 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5937 (mp0)
REVERT: R  140 MET cc_start: 0.7509 (tmm) cc_final: 0.7198 (tmm)
REVERT: R  182 LEU cc_start: 0.6933 (tp) cc_final: 0.6632 (tp)
REVERT: R  196 ARG cc_start: 0.5765 (mmt90) cc_final: 0.5436 (mmt90)
REVERT: R  199 PRO cc_start: 0.6768 (Cg_endo) cc_final: 0.6508 (Cg_exo)
REVERT: R  287 TRP cc_start: 0.6456 (m-10) cc_final: 0.5367 (m-10)
REVERT: R  395 ILE cc_start: 0.7922 (mm) cc_final: 0.7617 (mm)
  outliers start: 48
  outliers final: 36
  residues processed: 213
  average time/residue: 0.3198
  time to fit residues: 91.5659
Evaluate side-chains
  200 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 162
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   82 GLN
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  221 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue  125 GLU
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  301 THR
Chi-restraints excluded: chain R residue  343 THR
Chi-restraints excluded: chain R residue  363 GLU
Chi-restraints excluded: chain R residue  407 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0070
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.0004

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
N   1 GLN
N  39 GLN
P  19 GLN
R 204 GLN
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.166924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.136444 restraints weight = 15778.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.29
r_work: 0.3746 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11132  Z= 0.139
  Angle     :  0.658  11.396  15114  Z= 0.333
  Chirality :  0.043   0.180   1673
  Planarity :  0.004   0.044   1921
  Dihedral  :  5.586  57.601   1561
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 15.46 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.48 (0.22), residues: 1353
  helix:  0.47 (0.24), residues: 429
  sheet: -1.49 (0.28), residues: 314
  loop : -1.71 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 233 
 HIS   0.004   0.001   HIS R 166 
 PHE   0.023   0.001   PHE R 270 
 TYR   0.020   0.002   TYR R 141 
 ARG   0.006   0.001   ARG B  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  484)
  hydrogen bonds       : angle       5.32308 ( 1362)
  SS BOND              : bond        0.00263 (    8)
  SS BOND              : angle       0.92541 (   16)
  covalent geometry    : bond        0.00309 (11124)
  covalent geometry    : angle       0.65779 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 186
  time to evaluate  : 1.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6278 (pt0)
REVERT: A  264 ASN cc_start: 0.6740 (OUTLIER) cc_final: 0.6114 (t0)
REVERT: A  330 GLU cc_start: 0.2909 (OUTLIER) cc_final: 0.2502 (pp20)
REVERT: B   19 ARG cc_start: 0.7170 (mtp-110) cc_final: 0.6516 (mtp85)
REVERT: B   23 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7595 (ttmt)
REVERT: B  211 TRP cc_start: 0.8166 (m100) cc_final: 0.7916 (m100)
REVERT: E   84 THR cc_start: 0.6449 (t) cc_final: 0.6239 (m)
REVERT: P    7 THR cc_start: 0.7674 (m) cc_final: 0.7339 (p)
REVERT: R   37 GLN cc_start: 0.7010 (mm110) cc_final: 0.6293 (tm-30)
REVERT: R  109 TRP cc_start: 0.2256 (m100) cc_final: 0.1565 (m100)
REVERT: R  140 MET cc_start: 0.7521 (tmm) cc_final: 0.7195 (tmm)
REVERT: R  165 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6847 (pp)
REVERT: R  181 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6238 (ptm)
REVERT: R  182 LEU cc_start: 0.6766 (tp) cc_final: 0.6499 (tp)
REVERT: R  183 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5878 (ttm170)
REVERT: R  199 PRO cc_start: 0.6597 (Cg_endo) cc_final: 0.6308 (Cg_exo)
REVERT: R  287 TRP cc_start: 0.6409 (m-10) cc_final: 0.5174 (m-10)
REVERT: R  300 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5464 (mtt90)
REVERT: R  395 ILE cc_start: 0.7948 (mm) cc_final: 0.7612 (mm)
  outliers start: 48
  outliers final: 33
  residues processed: 222
  average time/residue: 0.2837
  time to fit residues: 86.9035
Evaluate side-chains
  207 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 167
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   82 GLN
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  356 VAL
Chi-restraints excluded: chain R residue  363 GLU
Chi-restraints excluded: chain R residue  407 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 30 optimal weight:    0.4980
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 119 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
N   1 GLN
N  39 GLN
P  19 GLN
R  93 HIS
R 204 GLN
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.169350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.138546 restraints weight = 15882.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.20
r_work: 0.3769 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11132  Z= 0.119
  Angle     :  0.629  11.032  15114  Z= 0.315
  Chirality :  0.043   0.271   1673
  Planarity :  0.004   0.045   1921
  Dihedral  :  5.195  56.704   1561
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.77 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.09 (0.23), residues: 1353
  helix:  0.91 (0.25), residues: 425
  sheet: -1.35 (0.28), residues: 316
  loop : -1.51 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 233 
 HIS   0.003   0.001   HIS R 166 
 PHE   0.021   0.001   PHE R 270 
 TYR   0.021   0.001   TYR R 141 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  484)
  hydrogen bonds       : angle       5.04680 ( 1362)
  SS BOND              : bond        0.00199 (    8)
  SS BOND              : angle       0.73115 (   16)
  covalent geometry    : bond        0.00258 (11124)
  covalent geometry    : angle       0.62933 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 192
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6055 (pt0)
REVERT: A  264 ASN cc_start: 0.6678 (OUTLIER) cc_final: 0.6137 (t0)
REVERT: A  330 GLU cc_start: 0.2921 (OUTLIER) cc_final: 0.2554 (pp20)
REVERT: B   19 ARG cc_start: 0.7263 (mtp-110) cc_final: 0.6599 (mtp85)
REVERT: B   52 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7431 (mtt-85)
REVERT: B  211 TRP cc_start: 0.8052 (m100) cc_final: 0.7760 (m100)
REVERT: B  336 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: E  128 MET cc_start: 0.7206 (mtm) cc_final: 0.6945 (mtm)
REVERT: E  148 ARG cc_start: 0.5559 (mmm-85) cc_final: 0.5270 (mmt90)
REVERT: G   19 LEU cc_start: 0.6443 (mt) cc_final: 0.6188 (mt)
REVERT: P    7 THR cc_start: 0.7591 (m) cc_final: 0.7324 (p)
REVERT: R   37 GLN cc_start: 0.7028 (mm110) cc_final: 0.6464 (tm-30)
REVERT: R  109 TRP cc_start: 0.2366 (m100) cc_final: 0.1621 (m100)
REVERT: R  165 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6670 (pp)
REVERT: R  181 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6115 (ptm)
REVERT: R  183 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5582 (ttm170)
REVERT: R  199 PRO cc_start: 0.6396 (Cg_endo) cc_final: 0.6124 (Cg_exo)
REVERT: R  203 ASP cc_start: 0.5329 (OUTLIER) cc_final: 0.4772 (p0)
REVERT: R  252 GLU cc_start: 0.4241 (OUTLIER) cc_final: 0.3913 (pm20)
REVERT: R  287 TRP cc_start: 0.6281 (m-10) cc_final: 0.5363 (m-10)
REVERT: R  300 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5606 (mtm110)
REVERT: R  395 ILE cc_start: 0.7972 (mm) cc_final: 0.7631 (mm)
REVERT: R  402 GLU cc_start: 0.4734 (tm-30) cc_final: 0.3949 (tt0)
REVERT: R  405 ARG cc_start: 0.5764 (tmm160) cc_final: 0.5435 (ttp80)
  outliers start: 47
  outliers final: 27
  residues processed: 227
  average time/residue: 0.4022
  time to fit residues: 124.9635
Evaluate side-chains
  217 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 1.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  363 GLU
Chi-restraints excluded: chain R residue  407 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 88 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0000
   chunk 133 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.7390

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

Flipped N/Q/H residues before XYZ refinement:
N   1 GLN
P  19 GLN
R  93 HIS
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.166906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.137026 restraints weight = 16044.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.18
r_work: 0.3726 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11132  Z= 0.164
  Angle     :  0.664  11.515  15114  Z= 0.335
  Chirality :  0.044   0.191   1673
  Planarity :  0.004   0.044   1921
  Dihedral  :  5.303  58.894   1560
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.99 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.13 (0.23), residues: 1353
  helix:  0.80 (0.25), residues: 438
  sheet: -1.34 (0.28), residues: 315
  loop : -1.53 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 233 
 HIS   0.005   0.001   HIS R 173 
 PHE   0.022   0.001   PHE R 270 
 TYR   0.022   0.002   TYR R 259 
 ARG   0.005   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  484)
  hydrogen bonds       : angle       5.04975 ( 1362)
  SS BOND              : bond        0.00300 (    8)
  SS BOND              : angle       0.85177 (   16)
  covalent geometry    : bond        0.00380 (11124)
  covalent geometry    : angle       0.66378 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 1.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6156 (pt0)
REVERT: A  264 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6125 (t0)
REVERT: A  330 GLU cc_start: 0.2998 (OUTLIER) cc_final: 0.2585 (pp20)
REVERT: B   19 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.6663 (mtp85)
REVERT: B   44 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6123 (pm20)
REVERT: B   52 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7477 (mtt-85)
REVERT: B  211 TRP cc_start: 0.8076 (m100) cc_final: 0.7823 (m100)
REVERT: B  336 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (mp)
REVERT: P    7 THR cc_start: 0.7698 (m) cc_final: 0.7399 (p)
REVERT: R   37 GLN cc_start: 0.6870 (mm110) cc_final: 0.6471 (tm-30)
REVERT: R   39 TRP cc_start: 0.6556 (t60) cc_final: 0.5936 (t60)
REVERT: R  109 TRP cc_start: 0.2291 (m100) cc_final: 0.1571 (m100)
REVERT: R  165 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6762 (pp)
REVERT: R  181 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6154 (ptm)
REVERT: R  199 PRO cc_start: 0.6409 (Cg_endo) cc_final: 0.6162 (Cg_exo)
REVERT: R  203 ASP cc_start: 0.5327 (OUTLIER) cc_final: 0.4771 (p0)
REVERT: R  252 GLU cc_start: 0.4333 (OUTLIER) cc_final: 0.3933 (pm20)
REVERT: R  287 TRP cc_start: 0.6382 (m-10) cc_final: 0.5075 (m-10)
REVERT: R  300 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5489 (mtt90)
REVERT: R  395 ILE cc_start: 0.7958 (mm) cc_final: 0.7619 (mm)
REVERT: R  405 ARG cc_start: 0.5738 (tmm160) cc_final: 0.3683 (ptm-80)
  outliers start: 48
  outliers final: 36
  residues processed: 211
  average time/residue: 0.5066
  time to fit residues: 145.6968
Evaluate side-chains
  211 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 165
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   82 GLN
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  356 VAL
Chi-restraints excluded: chain R residue  363 GLU
Chi-restraints excluded: chain R residue  407 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 117 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0020
   chunk 99 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0060
   chunk 95 optimal weight:    0.8980
   chunk 106 optimal weight:   20.0000
   overall best weight:    0.5204

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

Flipped N/Q/H residues before XYZ refinement:
N   1 GLN
N  39 GLN
P  19 GLN
R  93 HIS
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.170236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.141034 restraints weight = 16230.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 1.98
r_work: 0.3800 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11132  Z= 0.113
  Angle     :  0.611  11.350  15114  Z= 0.308
  Chirality :  0.042   0.177   1673
  Planarity :  0.004   0.045   1921
  Dihedral  :  5.014  55.787   1560
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 18.52 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.23), residues: 1353
  helix:  0.93 (0.25), residues: 439
  sheet: -1.25 (0.28), residues: 316
  loop : -1.38 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 233 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.021   0.001   PHE R 270 
 TYR   0.021   0.001   TYR R 141 
 ARG   0.005   0.000   ARG R 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  484)
  hydrogen bonds       : angle       4.87116 ( 1362)
  SS BOND              : bond        0.00148 (    8)
  SS BOND              : angle       0.61313 (   16)
  covalent geometry    : bond        0.00246 (11124)
  covalent geometry    : angle       0.61072 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 2.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6062 (t0)
REVERT: A  330 GLU cc_start: 0.2818 (OUTLIER) cc_final: 0.2439 (pp20)
REVERT: B   19 ARG cc_start: 0.7324 (mtp-110) cc_final: 0.6650 (mtp85)
REVERT: B   44 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6109 (pm20)
REVERT: B   52 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7438 (mtt-85)
REVERT: B  211 TRP cc_start: 0.7893 (m100) cc_final: 0.7626 (m100)
REVERT: B  336 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8057 (mp)
REVERT: E  161 TYR cc_start: 0.7966 (m-80) cc_final: 0.7546 (m-80)
REVERT: G   19 LEU cc_start: 0.6449 (mt) cc_final: 0.6198 (mt)
REVERT: P    7 THR cc_start: 0.7641 (m) cc_final: 0.7368 (p)
REVERT: R   37 GLN cc_start: 0.6748 (mm110) cc_final: 0.6486 (tm-30)
REVERT: R   39 TRP cc_start: 0.6694 (t60) cc_final: 0.6045 (t60)
REVERT: R  109 TRP cc_start: 0.2309 (m100) cc_final: 0.1608 (m100)
REVERT: R  161 LEU cc_start: 0.4006 (mt) cc_final: 0.3790 (mp)
REVERT: R  181 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.6162 (ptm)
REVERT: R  182 LEU cc_start: 0.6660 (tp) cc_final: 0.5667 (mp)
REVERT: R  183 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.5389 (ttm170)
REVERT: R  199 PRO cc_start: 0.6369 (Cg_endo) cc_final: 0.6090 (Cg_exo)
REVERT: R  203 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4720 (p0)
REVERT: R  252 GLU cc_start: 0.4305 (OUTLIER) cc_final: 0.3988 (pm20)
REVERT: R  287 TRP cc_start: 0.6191 (m-10) cc_final: 0.5258 (m-10)
REVERT: R  300 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5553 (mtt90)
REVERT: R  305 MET cc_start: 0.7241 (mmp) cc_final: 0.6543 (mmt)
REVERT: R  395 ILE cc_start: 0.7932 (mm) cc_final: 0.7606 (mm)
REVERT: R  405 ARG cc_start: 0.5511 (tmm160) cc_final: 0.3744 (ptm-80)
  outliers start: 43
  outliers final: 27
  residues processed: 219
  average time/residue: 0.4475
  time to fit residues: 131.5332
Evaluate side-chains
  210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 174
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  363 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 133 optimal weight:    4.9990
   chunk 132 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
N   1 GLN
P  19 GLN
R  93 HIS
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.169252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.139810 restraints weight = 15964.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.17
r_work: 0.3775 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3659 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11132  Z= 0.134
  Angle     :  0.633  10.588  15114  Z= 0.319
  Chirality :  0.043   0.207   1673
  Planarity :  0.004   0.045   1921
  Dihedral  :  5.026  57.373   1560
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.65 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -0.92 (0.23), residues: 1353
  helix:  0.89 (0.25), residues: 438
  sheet: -1.23 (0.28), residues: 317
  loop : -1.34 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 233 
 HIS   0.003   0.001   HIS R 166 
 PHE   0.021   0.001   PHE R 270 
 TYR   0.022   0.002   TYR R 200 
 ARG   0.007   0.000   ARG N  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  484)
  hydrogen bonds       : angle       4.88015 ( 1362)
  SS BOND              : bond        0.00270 (    8)
  SS BOND              : angle       0.74186 (   16)
  covalent geometry    : bond        0.00307 (11124)
  covalent geometry    : angle       0.63239 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5971 (pt0)
REVERT: A  264 ASN cc_start: 0.6570 (OUTLIER) cc_final: 0.6086 (t0)
REVERT: A  330 GLU cc_start: 0.2939 (OUTLIER) cc_final: 0.2516 (pp20)
REVERT: B   19 ARG cc_start: 0.7341 (mtp-110) cc_final: 0.6636 (mtp85)
REVERT: B   44 GLN cc_start: 0.6509 (OUTLIER) cc_final: 0.6140 (pm20)
REVERT: B   52 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7474 (mtt-85)
REVERT: B  211 TRP cc_start: 0.7938 (m100) cc_final: 0.7677 (m100)
REVERT: B  336 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (mp)
REVERT: E  161 TYR cc_start: 0.8057 (m-80) cc_final: 0.7688 (m-80)
REVERT: G   19 LEU cc_start: 0.6460 (mt) cc_final: 0.6230 (mt)
REVERT: R   37 GLN cc_start: 0.6749 (mm110) cc_final: 0.6484 (tm-30)
REVERT: R   39 TRP cc_start: 0.6525 (t60) cc_final: 0.5947 (t60)
REVERT: R  109 TRP cc_start: 0.2142 (m100) cc_final: 0.1479 (m100)
REVERT: R  161 LEU cc_start: 0.4171 (mt) cc_final: 0.3919 (mp)
REVERT: R  181 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6152 (ptm)
REVERT: R  182 LEU cc_start: 0.6664 (tp) cc_final: 0.5664 (mp)
REVERT: R  183 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5410 (ttm170)
REVERT: R  192 ARG cc_start: 0.4829 (ptm160) cc_final: 0.4457 (ptm160)
REVERT: R  199 PRO cc_start: 0.6321 (Cg_endo) cc_final: 0.6046 (Cg_exo)
REVERT: R  203 ASP cc_start: 0.5267 (OUTLIER) cc_final: 0.4698 (p0)
REVERT: R  252 GLU cc_start: 0.4343 (OUTLIER) cc_final: 0.3930 (pm20)
REVERT: R  287 TRP cc_start: 0.6297 (m-10) cc_final: 0.5298 (m-10)
REVERT: R  300 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5489 (mtt90)
REVERT: R  395 ILE cc_start: 0.7958 (mm) cc_final: 0.7623 (mm)
REVERT: R  405 ARG cc_start: 0.5482 (tmm160) cc_final: 0.3688 (ptm-80)
  outliers start: 43
  outliers final: 32
  residues processed: 206
  average time/residue: 0.2938
  time to fit residues: 81.4718
Evaluate side-chains
  210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 168
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  181 MET
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  363 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 126 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 132 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
N   1 GLN
R  93 HIS
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.167151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.136508 restraints weight = 16257.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.36
r_work: 0.3732 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11132  Z= 0.164
  Angle     :  0.669  12.347  15114  Z= 0.336
  Chirality :  0.044   0.197   1673
  Planarity :  0.004   0.045   1921
  Dihedral  :  5.218  59.762   1560
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.56 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.02 (0.23), residues: 1353
  helix:  0.81 (0.25), residues: 439
  sheet: -1.30 (0.28), residues: 316
  loop : -1.39 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 233 
 HIS   0.005   0.001   HIS R 173 
 PHE   0.022   0.002   PHE R 270 
 TYR   0.021   0.002   TYR R 259 
 ARG   0.005   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  484)
  hydrogen bonds       : angle       4.97852 ( 1362)
  SS BOND              : bond        0.00324 (    8)
  SS BOND              : angle       0.83289 (   16)
  covalent geometry    : bond        0.00381 (11124)
  covalent geometry    : angle       0.66833 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 174
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6074 (pt0)
REVERT: A  264 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6073 (t0)
REVERT: A  330 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2553 (pp20)
REVERT: B   19 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6679 (mtp85)
REVERT: B   44 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6166 (pm20)
REVERT: B   52 ARG cc_start: 0.7846 (ptp-110) cc_final: 0.7511 (mtt-85)
REVERT: B  211 TRP cc_start: 0.8052 (m100) cc_final: 0.7788 (m100)
REVERT: E  130 GLN cc_start: 0.6045 (mm110) cc_final: 0.5656 (mm110)
REVERT: E  161 TYR cc_start: 0.8086 (m-80) cc_final: 0.7831 (m-80)
REVERT: N   76 LYS cc_start: 0.8334 (mmtm) cc_final: 0.8098 (tptm)
REVERT: R   37 GLN cc_start: 0.6759 (mm110) cc_final: 0.6484 (tm-30)
REVERT: R   39 TRP cc_start: 0.6621 (t60) cc_final: 0.5934 (t60)
REVERT: R  109 TRP cc_start: 0.2221 (m100) cc_final: 0.1598 (m100)
REVERT: R  140 MET cc_start: 0.7584 (tmm) cc_final: 0.7298 (tmm)
REVERT: R  161 LEU cc_start: 0.4157 (mt) cc_final: 0.3863 (mp)
REVERT: R  183 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5658 (ttm170)
REVERT: R  192 ARG cc_start: 0.4999 (ptm160) cc_final: 0.4582 (ptm160)
REVERT: R  199 PRO cc_start: 0.6460 (Cg_endo) cc_final: 0.6191 (Cg_exo)
REVERT: R  204 GLN cc_start: 0.4192 (tp-100) cc_final: 0.3964 (tp-100)
REVERT: R  252 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.3964 (pm20)
REVERT: R  287 TRP cc_start: 0.6370 (m-10) cc_final: 0.5021 (m-10)
REVERT: R  300 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5519 (mtt90)
REVERT: R  395 ILE cc_start: 0.7970 (mm) cc_final: 0.7660 (mm)
REVERT: R  405 ARG cc_start: 0.5530 (tmm160) cc_final: 0.3627 (ptm-80)
  outliers start: 45
  outliers final: 34
  residues processed: 205
  average time/residue: 0.2806
  time to fit residues: 76.7395
Evaluate side-chains
  207 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 166
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  356 VAL
Chi-restraints excluded: chain R residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 125 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
N   1 GLN
N  39 GLN
P  19 GLN
R  93 HIS
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.167141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.136738 restraints weight = 16089.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.34
r_work: 0.3738 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3632 r_free = 0.3632    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11132  Z= 0.163
  Angle     :  0.665  13.161  15114  Z= 0.336
  Chirality :  0.044   0.185   1673
  Planarity :  0.004   0.046   1921
  Dihedral  :  5.249  59.893   1560
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.56 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.23), residues: 1353
  helix:  0.76 (0.25), residues: 438
  sheet: -1.35 (0.28), residues: 321
  loop : -1.35 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 233 
 HIS   0.005   0.001   HIS R 173 
 PHE   0.023   0.002   PHE R 270 
 TYR   0.021   0.002   TYR R 259 
 ARG   0.012   0.001   ARG N  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  484)
  hydrogen bonds       : angle       4.99411 ( 1362)
  SS BOND              : bond        0.00302 (    8)
  SS BOND              : angle       0.80528 (   16)
  covalent geometry    : bond        0.00379 (11124)
  covalent geometry    : angle       0.66479 (15098)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 176
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6094 (pt0)
REVERT: A  264 ASN cc_start: 0.6630 (OUTLIER) cc_final: 0.6124 (t0)
REVERT: A  330 GLU cc_start: 0.3098 (OUTLIER) cc_final: 0.2621 (pp20)
REVERT: B   19 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6691 (mtp85)
REVERT: B   44 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6217 (pm20)
REVERT: B   52 ARG cc_start: 0.7858 (ptp-110) cc_final: 0.7514 (mtt-85)
REVERT: B  211 TRP cc_start: 0.8038 (m100) cc_final: 0.7789 (m100)
REVERT: E  130 GLN cc_start: 0.6018 (mm110) cc_final: 0.5616 (mm110)
REVERT: G   21 MET cc_start: 0.6614 (tmm) cc_final: 0.6031 (tpp)
REVERT: N   76 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8079 (tptm)
REVERT: R   37 GLN cc_start: 0.6706 (mm110) cc_final: 0.6499 (tm-30)
REVERT: R   39 TRP cc_start: 0.6598 (t60) cc_final: 0.5918 (t60)
REVERT: R  109 TRP cc_start: 0.2270 (m100) cc_final: 0.1584 (m100)
REVERT: R  161 LEU cc_start: 0.4169 (mt) cc_final: 0.3874 (mp)
REVERT: R  183 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5343 (ttm170)
REVERT: R  192 ARG cc_start: 0.4862 (ptm160) cc_final: 0.4415 (ptm160)
REVERT: R  199 PRO cc_start: 0.6532 (Cg_endo) cc_final: 0.6263 (Cg_exo)
REVERT: R  204 GLN cc_start: 0.4137 (tp-100) cc_final: 0.3910 (tp-100)
REVERT: R  252 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.4030 (pm20)
REVERT: R  287 TRP cc_start: 0.6387 (m-10) cc_final: 0.4917 (m-10)
REVERT: R  300 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5536 (mtt90)
REVERT: R  305 MET cc_start: 0.7491 (mmp) cc_final: 0.6956 (mmt)
REVERT: R  395 ILE cc_start: 0.7931 (mm) cc_final: 0.7610 (mm)
REVERT: R  405 ARG cc_start: 0.5548 (tmm160) cc_final: 0.3654 (ptm-80)
  outliers start: 46
  outliers final: 35
  residues processed: 210
  average time/residue: 0.2790
  time to fit residues: 78.6155
Evaluate side-chains
  210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 168
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  204 ILE
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   57 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  142 THR
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 ARG
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  203 ASP
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  252 GLU
Chi-restraints excluded: chain R residue  297 TRP
Chi-restraints excluded: chain R residue  300 ARG
Chi-restraints excluded: chain R residue  356 VAL
Chi-restraints excluded: chain R residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 119 optimal weight:    0.0770
   chunk 107 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.7944

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   1 GLN
N  39 GLN
P  19 GLN
** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.167139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.136732 restraints weight = 16074.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 2.34
r_work: 0.3743 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3630 r_free = 0.3630    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11132  Z= 0.168
  Angle     :  0.710  18.884  15114  Z= 0.351
  Chirality :  0.045   0.308   1673
  Planarity :  0.005   0.105   1921
  Dihedral  :  5.315  59.538   1560
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.91 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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: -1.09 (0.23), residues: 1353
  helix:  0.71 (0.25), residues: 438
  sheet: -1.39 (0.27), residues: 321
  loop : -1.36 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R  90 
 HIS   0.005   0.001   HIS R 173 
 PHE   0.023   0.002   PHE R 270 
 TYR   0.021   0.002   TYR R 259 
 ARG   0.024   0.001   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  484)
  hydrogen bonds       : angle       5.00057 ( 1362)
  SS BOND              : bond        0.00314 (    8)
  SS BOND              : angle       0.80786 (   16)
  covalent geometry    : bond        0.00394 (11124)
  covalent geometry    : angle       0.70967 (15098)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8746.63 seconds
wall clock time: 159 minutes 52.01 seconds (9592.01 seconds total)