Starting phenix.real_space_refine
on Sun Jun  8 04:48:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wq3_32698/06_2025/7wq3_32698.cif"
  }
  resolution = 2.7
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5915      2.51       5
     N    1548      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9209
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2303
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 13, 'TRANS': 275}
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 117
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "R"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.45, per 1000 atoms: 0.59
  Number of scatterers: 9209
  At special positions: 0
  Unit cell: (110.16, 125.46, 123.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1685      8.00
     N    1548      7.00
     C    5915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 187 " 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: 2.10
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      39.7% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 4.618A  pdb=" N   VAL R  38 " --> pdb=" O   PHE R  34 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER R  61 " --> pdb=" O   VAL R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 98
      removed outlier: 3.754A  pdb=" N   ILE R  89 " --> pdb=" O   LEU R  85 " (cutoff:3.500A)
      Proline residue:  R  90  - end of helix
      removed outlier: 4.257A  pdb=" N   THR R  94 " --> pdb=" O   PRO R  90 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL R  95 " --> pdb=" O   PHE R  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR R  96 " --> pdb=" O   GLN R  92 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 139
      removed outlier: 4.015A  pdb=" N   ILE R 107 " --> pdb=" O   LEU R 103 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   HIS R 112 " --> pdb=" O   CYS R 108 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE R 137 " --> pdb=" O   ARG R 133 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   HIS R 139 " --> pdb=" O   VAL R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 142 through 147
    Processing helix  chain 'R' and resid 148 through 167
    Processing helix  chain 'R' and resid 167 through 174
      removed outlier: 3.656A  pdb=" N   ALA R 171 " --> pdb=" O   ALA R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 209
      removed outlier: 3.715A  pdb=" N   ALA R 199 " --> pdb=" O   ARG R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 231
    Processing helix  chain 'R' and resid 235 through 260
      removed outlier: 4.429A  pdb=" N   TRP R 260 " --> pdb=" O   PHE R 256 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 272
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.780A  pdb=" N   SER R 296 " --> pdb=" O   ALA R 292 " (cutoff:3.500A)
      Proline residue:  R 300  - end of helix
    Processing helix  chain 'R' and resid 307 through 318
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 5.078A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.166A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 232'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.543A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.360A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.631A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.631A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.852A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.605A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.884A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.184A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.789A  pdb=" N   ASP S 223 " --> pdb=" O   GLU S 220 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 220 through 224'
    Processing helix  chain 'L' and resid 3 through 12
    Processing sheet with id=AA1, first strand: chain 'R' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.299A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.973A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.033A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.010A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.789A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.318A  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: 7.177A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.121A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.620A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.292A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.292A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.928A  pdb=" N   THR S 141 " --> pdb=" O   ARG S 160 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG S 160 " --> pdb=" O   THR S 141 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.028A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2915
        1.34 -     1.46: 2281
        1.46 -     1.58: 4113
        1.58 -     1.70: 25
        1.70 -     1.81: 91
  Bond restraints: 9425
  Sorted by residual:
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.652 -0.320 2.00e-02 2.50e+03 2.56e+02
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 405 "
       pdb=" C6  CLR R 405 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 403 "
       pdb=" C6  CLR R 403 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 404 "
       pdb=" C6  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.332  1.650 -0.318 2.00e-02 2.50e+03 2.53e+02
  ... (remaining 9420 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 12667
        2.66 -     5.32: 91
        5.32 -     7.98: 19
        7.98 -    10.64: 10
       10.64 -    13.30: 10
  Bond angle restraints: 12797
  Sorted by residual:
  angle pdb=" C5  CLR R 405 "
        pdb=" C6  CLR R 405 "
        pdb=" C7  CLR R 405 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 403 "
        pdb=" C6  CLR R 403 "
        pdb=" C7  CLR R 403 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C5  CLR R 402 "
        pdb=" C6  CLR R 402 "
        pdb=" C7  CLR R 402 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C5  CLR R 404 "
        pdb=" C6  CLR R 404 "
        pdb=" C7  CLR R 404 "
      ideal   model   delta    sigma   weight residual
     125.11  111.82   13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C4  CLR R 401 "
        pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     120.33  107.93   12.40 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 12792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 5564
       15.56 -    31.12: 165
       31.12 -    46.68: 53
       46.68 -    62.24: 23
       62.24 -    77.79: 3
  Dihedral angle restraints: 5808
    sinusoidal: 2443
      harmonic: 3365
  Sorted by residual:
  dihedral pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
           pdb=" CB  ARG S 191 "
           pdb=" CG  ARG S 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.85   59.85     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   PHE B 234 "
           pdb=" CA  PHE B 234 "
           pdb=" CB  PHE B 234 "
           pdb=" CG  PHE B 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.95  -57.05     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   PHE R 114 "
           pdb=" CA  PHE R 114 "
           pdb=" CB  PHE R 114 "
           pdb=" CG  PHE R 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.13   53.13     3      1.50e+01 4.44e-03 9.18e+00
  ... (remaining 5805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1408
       0.112 -    0.223: 29
       0.223 -    0.335: 11
       0.335 -    0.446: 4
       0.446 -    0.558: 5
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" C13 CLR R 405 "
            pdb=" C12 CLR R 405 "
            pdb=" C14 CLR R 405 "
            pdb=" C17 CLR R 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.37   -0.56 2.00e-01 2.50e+01 7.78e+00
  chirality pdb=" C13 CLR R 404 "
            pdb=" C12 CLR R 404 "
            pdb=" C14 CLR R 404 "
            pdb=" C17 CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.55 2.00e-01 2.50e+01 7.69e+00
  ... (remaining 1454 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 299 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO R 300 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO S  41 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO B 236 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 435
        2.73 -     3.27: 9049
        3.27 -     3.82: 14930
        3.82 -     4.36: 17758
        4.36 -     4.90: 31232
  Nonbonded interactions: 73404
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 248 "
            pdb=" OD1 ASP A 251 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   PHE S  29 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.269 3.040
  ... (remaining 73399 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.500
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4588
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      :  0.011   0.320   9426  Z= 0.539
  Angle     :  0.724  13.301  12799  Z= 0.335
  Chirality :  0.061   0.558   1457
  Planarity :  0.003   0.032   1586
  Dihedral  :  9.420  77.794   3633
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  2.43 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -1.34 (0.23), residues: 1144
  helix:  0.07 (0.25), residues: 408
  sheet: -1.00 (0.27), residues: 292
  loop : -1.59 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.008   0.001   PHE A 274 
 TYR   0.006   0.001   TYR S 102 
 ARG   0.002   0.000   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14093 (  460)
  hydrogen bonds       : angle       4.96401 ( 1311)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.37252 (    2)
  covalent geometry    : bond        0.01071 ( 9425)
  covalent geometry    : angle       0.72428 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 227
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 ASN cc_start: 0.6883 (m110) cc_final: 0.6622 (m110)
REVERT: R  244 LYS cc_start: 0.6246 (mttt) cc_final: 0.5999 (mtmm)
REVERT: A  248 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6377 (tmmm)
REVERT: A  266 LEU cc_start: 0.5029 (tp) cc_final: 0.4807 (tm)
REVERT: A  276 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0)
REVERT: A  305 CYS cc_start: 0.6720 (m) cc_final: 0.6438 (m)
REVERT: A  314 LYS cc_start: 0.6025 (mttt) cc_final: 0.5625 (tppt)
REVERT: A  342 VAL cc_start: 0.6855 (t) cc_final: 0.6526 (m)
REVERT: G   20 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6256 (pttm)
REVERT: G   60 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6097 (Cg_exo)
REVERT: S   53 SER cc_start: 0.6534 (t) cc_final: 0.6274 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 231
  average time/residue: 1.0246
  time to fit residues: 255.2121
Evaluate side-chains
  136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0170
   chunk 65 optimal weight:    3.9990
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
R  71 ASN
R 173 HIS
R 190 GLN
A 204 GLN
B  91 HIS
B 142 HIS
B 176 GLN
G  18 GLN
G  59 ASN
S  39 GLN
S 194 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.196991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.168634 restraints weight = 11616.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.83
r_work: 0.3869 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3764 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9426  Z= 0.169
  Angle     :  0.691  10.469  12799  Z= 0.349
  Chirality :  0.044   0.173   1457
  Planarity :  0.005   0.054   1586
  Dihedral  :  6.943  55.688   1574
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.94 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.10 (0.24), residues: 1144
  helix:  1.30 (0.27), residues: 396
  sheet: -0.31 (0.28), residues: 288
  loop : -1.06 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP S  36 
 HIS   0.014   0.002   HIS R 173 
 PHE   0.028   0.002   PHE R  91 
 TYR   0.015   0.002   TYR G  40 
 ARG   0.006   0.001   ARG S 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  460)
  hydrogen bonds       : angle       4.25287 ( 1311)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       1.79134 (    2)
  covalent geometry    : bond        0.00350 ( 9425)
  covalent geometry    : angle       0.69118 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
REVERT: R   78 SER cc_start: 0.7236 (m) cc_final: 0.6466 (p)
REVERT: R  129 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7008 (mtm)
REVERT: A  198 MET cc_start: 0.8000 (mtp) cc_final: 0.7783 (mtm)
REVERT: A  248 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7538 (tmmm)
REVERT: A  305 CYS cc_start: 0.7634 (m) cc_final: 0.7360 (m)
REVERT: B  134 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7358 (mtp-110)
REVERT: B  190 LEU cc_start: 0.8606 (mt) cc_final: 0.8319 (pp)
REVERT: B  219 ARG cc_start: 0.8460 (mmt180) cc_final: 0.8066 (mpt-90)
REVERT: G   38 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5683 (mmm)
REVERT: S   46 GLU cc_start: 0.7595 (pt0) cc_final: 0.7329 (pt0)
REVERT: S   58 ILE cc_start: 0.6449 (mt) cc_final: 0.6031 (mt)
REVERT: S   83 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8088 (ptp)
  outliers start: 30
  outliers final: 10
  residues processed: 200
  average time/residue: 1.0561
  time to fit residues: 227.3437
Evaluate side-chains
  127 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  129 MET
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  164 SER
Chi-restraints excluded: chain S residue  204 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0980
   chunk 81 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
R 228 HIS
R 299 ASN
A 204 GLN
B  88 ASN
B 125 ASN
B 340 ASN
L   5 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.183908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150922 restraints weight = 10822.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.00
r_work: 0.3587 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.7231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9426  Z= 0.135
  Angle     :  0.577   7.891  12799  Z= 0.294
  Chirality :  0.041   0.144   1457
  Planarity :  0.004   0.035   1586
  Dihedral  :  5.886  40.371   1574
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 13.97 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  0.56 (0.25), residues: 1144
  helix:  2.00 (0.28), residues: 394
  sheet:  0.04 (0.29), residues: 283
  loop : -0.80 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  63 
 HIS   0.011   0.001   HIS S  35 
 PHE   0.016   0.001   PHE B 292 
 TYR   0.009   0.001   TYR S 173 
 ARG   0.009   0.001   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03900 (  460)
  hydrogen bonds       : angle       3.86120 ( 1311)
  SS BOND              : bond        0.00501 (    1)
  SS BOND              : angle       1.79078 (    2)
  covalent geometry    : bond        0.00291 ( 9425)
  covalent geometry    : angle       0.57710 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 164
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  115 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7263 (p90)
REVERT: A   17 LYS cc_start: 0.7837 (mttt) cc_final: 0.7595 (mtmt)
REVERT: A   28 GLU cc_start: 0.7658 (tt0) cc_final: 0.7073 (mt-10)
REVERT: A  209 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7545 (mptt)
REVERT: B   16 ASN cc_start: 0.6460 (m-40) cc_final: 0.6200 (m110)
REVERT: B   98 SER cc_start: 0.8783 (m) cc_final: 0.8485 (t)
REVERT: B  134 ARG cc_start: 0.8323 (mtp180) cc_final: 0.7657 (mtp-110)
REVERT: B  137 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7526 (tpp-160)
REVERT: B  215 GLU cc_start: 0.7911 (mp0) cc_final: 0.7623 (mt-10)
REVERT: B  268 ASN cc_start: 0.7329 (t0) cc_final: 0.6958 (m-40)
REVERT: S    3 GLN cc_start: 0.8240 (tm-30) cc_final: 0.8000 (tt0)
REVERT: S   46 GLU cc_start: 0.8451 (pt0) cc_final: 0.8129 (pt0)
REVERT: S  183 GLN cc_start: 0.6044 (mm110) cc_final: 0.5795 (mp-120)
REVERT: S  191 ARG cc_start: 0.3000 (OUTLIER) cc_final: 0.2019 (tpp80)
  outliers start: 42
  outliers final: 14
  residues processed: 188
  average time/residue: 1.1749
  time to fit residues: 236.4956
Evaluate side-chains
  150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  135 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  191 ARG
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0970
   chunk 87 optimal weight:    0.0870
   chunk 83 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 76 optimal weight:    0.2980
   overall best weight:    0.4156

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

Flipped N/Q/H residues before XYZ refinement:
R 190 GLN
A 204 GLN
A 269 ASN
B 156 GLN
B 176 GLN
B 340 ASN
S  39 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.148244 restraints weight = 10715.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.97
r_work: 0.3545 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.7935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9426  Z= 0.095
  Angle     :  0.479   7.639  12799  Z= 0.247
  Chirality :  0.040   0.142   1457
  Planarity :  0.003   0.038   1586
  Dihedral  :  5.322  59.492   1574
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.81 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.26), residues: 1144
  helix:  2.42 (0.28), residues: 390
  sheet:  0.20 (0.30), residues: 283
  loop : -0.49 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 228 
 PHE   0.011   0.001   PHE R 115 
 TYR   0.009   0.001   TYR S 173 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02970 (  460)
  hydrogen bonds       : angle       3.77357 ( 1311)
  SS BOND              : bond        0.00293 (    1)
  SS BOND              : angle       1.44140 (    2)
  covalent geometry    : bond        0.00197 ( 9425)
  covalent geometry    : angle       0.47908 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.936 
Fit side-chains
REVERT: R  252 VAL cc_start: 0.7291 (p) cc_final: 0.6843 (m)
REVERT: A   28 GLU cc_start: 0.7835 (tt0) cc_final: 0.7312 (mt-10)
REVERT: A  209 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7666 (mptt)
REVERT: B   16 ASN cc_start: 0.6613 (m-40) cc_final: 0.6221 (m110)
REVERT: B   98 SER cc_start: 0.8814 (m) cc_final: 0.8512 (t)
REVERT: B  134 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7687 (mtp-110)
REVERT: B  215 GLU cc_start: 0.7923 (mp0) cc_final: 0.7449 (mt-10)
REVERT: B  268 ASN cc_start: 0.7411 (t0) cc_final: 0.7127 (m-40)
REVERT: G   58 GLU cc_start: 0.6964 (mp0) cc_final: 0.6212 (tm-30)
REVERT: S    3 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8024 (OUTLIER)
REVERT: S   46 GLU cc_start: 0.8476 (pt0) cc_final: 0.8120 (pt0)
REVERT: S   71 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7873 (p)
REVERT: S  140 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6807 (mmm)
REVERT: S  160 ARG cc_start: 0.7344 (ptm-80) cc_final: 0.6122 (mtm-85)
REVERT: S  183 GLN cc_start: 0.6165 (mm110) cc_final: 0.5862 (mp-120)
  outliers start: 36
  outliers final: 13
  residues processed: 166
  average time/residue: 1.2116
  time to fit residues: 215.8327
Evaluate side-chains
  138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  307 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 85 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 204 GLN
B  32 GLN
B 239 ASN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.178820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.147459 restraints weight = 11370.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 1.87
r_work: 0.3599 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.9066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9426  Z= 0.113
  Angle     :  0.508   6.631  12799  Z= 0.266
  Chirality :  0.041   0.167   1457
  Planarity :  0.003   0.044   1586
  Dihedral  :  4.927  51.553   1574
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.62 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1144
  helix:  2.43 (0.27), residues: 391
  sheet:  0.31 (0.31), residues: 284
  loop : -0.42 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R 228 
 PHE   0.015   0.001   PHE R 115 
 TYR   0.008   0.001   TYR S  95 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  460)
  hydrogen bonds       : angle       3.83141 ( 1311)
  SS BOND              : bond        0.00509 (    1)
  SS BOND              : angle       1.59172 (    2)
  covalent geometry    : bond        0.00248 ( 9425)
  covalent geometry    : angle       0.50796 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 1.090 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.6327 (pp) cc_final: 0.5984 (mt)
REVERT: R   91 PHE cc_start: 0.6495 (m-10) cc_final: 0.6174 (m-10)
REVERT: R  252 VAL cc_start: 0.7584 (OUTLIER) cc_final: 0.7266 (m)
REVERT: R  261 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7662 (tm)
REVERT: A   22 ASN cc_start: 0.8255 (m-40) cc_final: 0.8043 (m110)
REVERT: A   25 GLU cc_start: 0.7573 (tt0) cc_final: 0.6885 (tm-30)
REVERT: A   28 GLU cc_start: 0.7874 (tt0) cc_final: 0.7560 (mt-10)
REVERT: A  209 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7901 (mptt)
REVERT: A  273 LEU cc_start: 0.7698 (tp) cc_final: 0.7299 (tp)
REVERT: B   16 ASN cc_start: 0.6813 (m-40) cc_final: 0.6197 (m110)
REVERT: B   20 ASP cc_start: 0.7829 (m-30) cc_final: 0.7600 (m-30)
REVERT: B   78 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7642 (mtpp)
REVERT: B  130 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6978 (mp0)
REVERT: B  134 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7929 (ptp90)
REVERT: B  175 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7767 (mp10)
REVERT: B  215 GLU cc_start: 0.7897 (mp0) cc_final: 0.7686 (mt-10)
REVERT: B  296 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (p)
REVERT: G   58 GLU cc_start: 0.7128 (mp0) cc_final: 0.6319 (tm-30)
REVERT: S   46 GLU cc_start: 0.8697 (pt0) cc_final: 0.8311 (pt0)
REVERT: S   65 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7197 (tttp)
REVERT: S   71 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7953 (p)
REVERT: S   83 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8098 (ptm)
REVERT: S  140 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.6737 (mmm)
REVERT: S  160 ARG cc_start: 0.7546 (ptm-80) cc_final: 0.6364 (mtm-85)
REVERT: S  183 GLN cc_start: 0.6902 (mm110) cc_final: 0.6600 (mp-120)
  outliers start: 41
  outliers final: 15
  residues processed: 174
  average time/residue: 1.4318
  time to fit residues: 266.4566
Evaluate side-chains
  156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  151 ASN
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 103 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:
A  52 GLN
A 204 GLN
A 269 ASN
B  32 GLN
B 239 ASN
S 171 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.171919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.140812 restraints weight = 11277.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.87
r_work: 0.3514 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          1.0262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9426  Z= 0.138
  Angle     :  0.571   7.412  12799  Z= 0.297
  Chirality :  0.042   0.136   1457
  Planarity :  0.004   0.059   1586
  Dihedral  :  5.287  59.663   1574
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.02 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1144
  helix:  2.42 (0.27), residues: 397
  sheet:  0.27 (0.30), residues: 290
  loop : -0.53 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.024   0.002   PHE R 115 
 TYR   0.009   0.001   TYR S  95 
 ARG   0.003   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  460)
  hydrogen bonds       : angle       3.97126 ( 1311)
  SS BOND              : bond        0.00772 (    1)
  SS BOND              : angle       1.76964 (    2)
  covalent geometry    : bond        0.00316 ( 9425)
  covalent geometry    : angle       0.57068 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 148
  time to evaluate  : 1.637 
Fit side-chains
REVERT: R   78 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7818 (m)
REVERT: R  252 VAL cc_start: 0.7790 (p) cc_final: 0.7528 (m)
REVERT: A   24 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7813 (mtm110)
REVERT: A   25 GLU cc_start: 0.7752 (tt0) cc_final: 0.7026 (tm-30)
REVERT: A   28 GLU cc_start: 0.7884 (tt0) cc_final: 0.7534 (mt-10)
REVERT: A  209 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7957 (mptt)
REVERT: A  272 ASP cc_start: 0.6960 (m-30) cc_final: 0.6713 (m-30)
REVERT: A  273 LEU cc_start: 0.7959 (tp) cc_final: 0.7568 (tp)
REVERT: B   16 ASN cc_start: 0.6963 (m-40) cc_final: 0.6327 (m110)
REVERT: B   42 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6581 (tmt170)
REVERT: B   46 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7670 (mmt90)
REVERT: B  130 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7252 (mp0)
REVERT: B  135 VAL cc_start: 0.8968 (t) cc_final: 0.8697 (p)
REVERT: B  215 GLU cc_start: 0.7992 (mp0) cc_final: 0.7731 (mt-10)
REVERT: B  325 MET cc_start: 0.8709 (tpp) cc_final: 0.8484 (mmt)
REVERT: G   58 GLU cc_start: 0.7283 (mp0) cc_final: 0.6401 (tm-30)
REVERT: S   18 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7412 (mmt180)
REVERT: S   46 GLU cc_start: 0.8707 (pt0) cc_final: 0.8317 (pt0)
REVERT: S   65 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7211 (tttm)
REVERT: S   78 THR cc_start: 0.8046 (t) cc_final: 0.7483 (m)
REVERT: S  113 GLN cc_start: 0.8072 (mm110) cc_final: 0.7829 (mm110)
REVERT: S  140 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.6874 (mmm)
REVERT: S  160 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6781 (mtm-85)
  outliers start: 46
  outliers final: 15
  residues processed: 172
  average time/residue: 1.5277
  time to fit residues: 281.7289
Evaluate side-chains
  157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  261 LEU
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  160 ARG
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 204 GLN
B  32 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.172592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.141492 restraints weight = 11389.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.89
r_work: 0.3530 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          1.0482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9426  Z= 0.112
  Angle     :  0.521   8.885  12799  Z= 0.268
  Chirality :  0.041   0.140   1457
  Planarity :  0.004   0.062   1586
  Dihedral  :  4.900  57.089   1574
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.65 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.18 (0.26), residues: 1144
  helix:  2.54 (0.27), residues: 392
  sheet:  0.34 (0.30), residues: 284
  loop : -0.43 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 228 
 PHE   0.020   0.001   PHE R 115 
 TYR   0.012   0.001   TYR R  84 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  460)
  hydrogen bonds       : angle       3.81480 ( 1311)
  SS BOND              : bond        0.00562 (    1)
  SS BOND              : angle       1.36527 (    2)
  covalent geometry    : bond        0.00256 ( 9425)
  covalent geometry    : angle       0.52125 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 1.096 
Fit side-chains
REVERT: R   78 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7661 (m)
REVERT: R  252 VAL cc_start: 0.7799 (p) cc_final: 0.7540 (m)
REVERT: A   25 GLU cc_start: 0.7804 (tt0) cc_final: 0.7548 (tt0)
REVERT: A   28 GLU cc_start: 0.7913 (tt0) cc_final: 0.7548 (mt-10)
REVERT: A  209 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7995 (mptt)
REVERT: B   16 ASN cc_start: 0.6931 (m-40) cc_final: 0.6450 (m110)
REVERT: B   46 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7622 (mmt90)
REVERT: B  130 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7288 (mp0)
REVERT: B  135 VAL cc_start: 0.8963 (t) cc_final: 0.8674 (p)
REVERT: B  172 GLU cc_start: 0.7766 (tp30) cc_final: 0.7431 (mt-10)
REVERT: B  296 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8438 (p)
REVERT: B  325 MET cc_start: 0.8700 (tpp) cc_final: 0.8479 (mmt)
REVERT: G   58 GLU cc_start: 0.7282 (mp0) cc_final: 0.6351 (tm-30)
REVERT: S   18 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7393 (mmt180)
REVERT: S   46 GLU cc_start: 0.8762 (pt0) cc_final: 0.8461 (pt0)
REVERT: S   65 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7458 (ttpt)
REVERT: S  140 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.6862 (mmm)
REVERT: S  160 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.6819 (mtm-85)
  outliers start: 29
  outliers final: 15
  residues processed: 154
  average time/residue: 1.1905
  time to fit residues: 196.1402
Evaluate side-chains
  153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 101 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0870
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.0960

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 204 GLN
B  32 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.169735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.139503 restraints weight = 11577.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 1.90
r_work: 0.3498 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          1.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   9426  Z= 0.129
  Angle     :  0.544   7.446  12799  Z= 0.282
  Chirality :  0.042   0.138   1457
  Planarity :  0.004   0.055   1586
  Dihedral  :  4.940  59.947   1574
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.95 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.26), residues: 1144
  helix:  2.47 (0.27), residues: 392
  sheet:  0.38 (0.30), residues: 283
  loop : -0.48 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.024   0.002   PHE R 115 
 TYR   0.009   0.001   TYR S  59 
 ARG   0.006   0.000   ARG R 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  460)
  hydrogen bonds       : angle       3.92072 ( 1311)
  SS BOND              : bond        0.00672 (    1)
  SS BOND              : angle       1.39230 (    2)
  covalent geometry    : bond        0.00307 ( 9425)
  covalent geometry    : angle       0.54374 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.926 
Fit side-chains
REVERT: R  252 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7677 (m)
REVERT: R  271 GLU cc_start: 0.7577 (tp30) cc_final: 0.7258 (mm-30)
REVERT: A   25 GLU cc_start: 0.7813 (tt0) cc_final: 0.7580 (tt0)
REVERT: A   28 GLU cc_start: 0.7937 (tt0) cc_final: 0.7646 (mt-10)
REVERT: A  209 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8011 (mptt)
REVERT: B   16 ASN cc_start: 0.6915 (m-40) cc_final: 0.6556 (m110)
REVERT: B   46 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7654 (mmt90)
REVERT: B  130 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7302 (mp0)
REVERT: B  135 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8701 (p)
REVERT: B  325 MET cc_start: 0.8692 (tpp) cc_final: 0.8453 (mmt)
REVERT: G   46 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7924 (pmtt)
REVERT: G   58 GLU cc_start: 0.7366 (mp0) cc_final: 0.6368 (tm-30)
REVERT: S   18 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7360 (mmt180)
REVERT: S   46 GLU cc_start: 0.8703 (pt0) cc_final: 0.8337 (pt0)
REVERT: S   65 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7464 (ttpt)
REVERT: S   78 THR cc_start: 0.8189 (t) cc_final: 0.7681 (m)
REVERT: S  118 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7784 (p)
REVERT: S  140 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.6979 (mmm)
  outliers start: 34
  outliers final: 18
  residues processed: 155
  average time/residue: 1.1386
  time to fit residues: 189.7879
Evaluate side-chains
  153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  166 MET
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  192 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 109 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
G  18 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.171829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.141224 restraints weight = 11359.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.85
r_work: 0.3517 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          1.0952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9426  Z= 0.111
  Angle     :  0.527   9.115  12799  Z= 0.270
  Chirality :  0.041   0.137   1457
  Planarity :  0.004   0.053   1586
  Dihedral  :  4.749  58.522   1574
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.26 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.18 (0.26), residues: 1144
  helix:  2.55 (0.27), residues: 391
  sheet:  0.28 (0.30), residues: 290
  loop : -0.39 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 228 
 PHE   0.019   0.001   PHE R 115 
 TYR   0.008   0.001   TYR A 302 
 ARG   0.006   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 (  460)
  hydrogen bonds       : angle       3.84041 ( 1311)
  SS BOND              : bond        0.00574 (    1)
  SS BOND              : angle       1.41241 (    2)
  covalent geometry    : bond        0.00258 ( 9425)
  covalent geometry    : angle       0.52683 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.938 
Fit side-chains
REVERT: R   51 ASN cc_start: 0.7364 (m-40) cc_final: 0.6898 (m110)
REVERT: R  252 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7627 (m)
REVERT: R  271 GLU cc_start: 0.7563 (tp30) cc_final: 0.7299 (mm-30)
REVERT: R  308 GLU cc_start: 0.7882 (mp0) cc_final: 0.7405 (mt-10)
REVERT: A   25 GLU cc_start: 0.7794 (tt0) cc_final: 0.7518 (tt0)
REVERT: A   28 GLU cc_start: 0.7885 (tt0) cc_final: 0.7568 (mt-10)
REVERT: A  209 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8033 (mptt)
REVERT: B   16 ASN cc_start: 0.6765 (m-40) cc_final: 0.6477 (m110)
REVERT: B   46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7614 (mtp180)
REVERT: B  130 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7252 (mp0)
REVERT: B  135 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8676 (p)
REVERT: B  296 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8455 (p)
REVERT: B  325 MET cc_start: 0.8655 (tpp) cc_final: 0.8443 (mmt)
REVERT: G   58 GLU cc_start: 0.7361 (mp0) cc_final: 0.6377 (tm-30)
REVERT: S   46 GLU cc_start: 0.8698 (pt0) cc_final: 0.8423 (pt0)
REVERT: S   65 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7485 (ttpt)
REVERT: S   78 THR cc_start: 0.8146 (t) cc_final: 0.7669 (m)
REVERT: S  118 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7783 (p)
REVERT: S  160 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6961 (mtm-85)
REVERT: S  192 MET cc_start: 0.4787 (mpp) cc_final: 0.2950 (mtm)
  outliers start: 37
  outliers final: 18
  residues processed: 160
  average time/residue: 1.1848
  time to fit residues: 203.9290
Evaluate side-chains
  157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  254 VAL
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  160 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 108 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0020
   chunk 99 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
B 268 ASN
G  18 GLN
S  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.173566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.143554 restraints weight = 11389.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.85
r_work: 0.3539 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          1.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072   9426  Z= 0.099
  Angle     :  0.513   7.773  12799  Z= 0.264
  Chirality :  0.040   0.136   1457
  Planarity :  0.004   0.053   1586
  Dihedral  :  4.577  56.706   1574
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 22.06 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1144
  helix:  2.56 (0.27), residues: 391
  sheet:  0.38 (0.30), residues: 281
  loop : -0.35 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 228 
 PHE   0.017   0.001   PHE R 282 
 TYR   0.010   0.001   TYR S  59 
 ARG   0.009   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 (  460)
  hydrogen bonds       : angle       3.77289 ( 1311)
  SS BOND              : bond        0.00434 (    1)
  SS BOND              : angle       1.04932 (    2)
  covalent geometry    : bond        0.00224 ( 9425)
  covalent geometry    : angle       0.51267 (12797)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 1.071 
Fit side-chains
REVERT: R   51 ASN cc_start: 0.7223 (m-40) cc_final: 0.6791 (m110)
REVERT: R  252 VAL cc_start: 0.7811 (p) cc_final: 0.7579 (m)
REVERT: R  271 GLU cc_start: 0.7546 (tp30) cc_final: 0.7327 (mm-30)
REVERT: R  308 GLU cc_start: 0.7880 (mp0) cc_final: 0.7400 (mt-10)
REVERT: A   25 GLU cc_start: 0.7772 (tt0) cc_final: 0.7511 (tt0)
REVERT: A   28 GLU cc_start: 0.7840 (tt0) cc_final: 0.7533 (mt-10)
REVERT: B   46 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7575 (mtp180)
REVERT: B  130 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7171 (mp0)
REVERT: B  172 GLU cc_start: 0.7817 (tp30) cc_final: 0.7488 (pt0)
REVERT: G   42 GLU cc_start: 0.7639 (tm-30) cc_final: 0.6413 (mm-30)
REVERT: G   58 GLU cc_start: 0.7331 (mp0) cc_final: 0.6360 (tm-30)
REVERT: S   13 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8378 (mm110)
REVERT: S   46 GLU cc_start: 0.8758 (pt0) cc_final: 0.8507 (pt0)
REVERT: S   65 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7496 (ttpt)
REVERT: S   78 THR cc_start: 0.8059 (t) cc_final: 0.7648 (m)
REVERT: S  118 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7750 (p)
REVERT: S  192 MET cc_start: 0.4758 (mpp) cc_final: 0.2949 (mtm)
  outliers start: 28
  outliers final: 18
  residues processed: 159
  average time/residue: 1.1068
  time to fit residues: 189.2999
Evaluate side-chains
  154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 SER
Chi-restraints excluded: chain R residue  115 PHE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  32 GLN
G  18 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.167963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.136891 restraints weight = 11324.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.95
r_work: 0.3458 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          1.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   9426  Z= 0.160
  Angle     :  0.592   9.028  12799  Z= 0.306
  Chirality :  0.043   0.143   1457
  Planarity :  0.004   0.054   1586
  Dihedral  :  4.995  59.152   1574
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.06 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.10 (0.25), residues: 1144
  helix:  2.38 (0.27), residues: 392
  sheet:  0.45 (0.31), residues: 276
  loop : -0.48 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 211 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.028   0.002   PHE R 115 
 TYR   0.011   0.002   TYR S  95 
 ARG   0.006   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  460)
  hydrogen bonds       : angle       4.01534 ( 1311)
  SS BOND              : bond        0.00853 (    1)
  SS BOND              : angle       1.65144 (    2)
  covalent geometry    : bond        0.00387 ( 9425)
  covalent geometry    : angle       0.59186 (12797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8424.12 seconds
wall clock time: 147 minutes 32.68 seconds (8852.68 seconds total)